Hello,

I deal with technologies that produce with very wide datasets:
- NanoStrings data with 700 genes (1000 rows * 700 columns)
- OmniExpress Illumina SNPs genotyping with 650k SNPs (1000 rows * 650k columns)

I would be interested to integrate these datasets into my study. What would be the best practices to deal with such wide data format in LabKey? Knowing that I have not be able to import them as such from the original file.
Is it a good idea to melt them ? Shall I split them in some ways ? Is it recommended to use the API to upload these datasets ?
I would be glad to hear from your experience.


best wishes,

Vincent.

I have added a custom field "cell_count_moxi" to the specimen repository, and I want to use rollups for the grouped vial view. So, I added cell_count_moxi to both the "SpecimenEvent" and "Vial" field lists. Then I tried to add a rollup field to the "Specimen" field list. If I add "Totalcell_count_moxi" that works. However, "Maxcell_count_moxi" and "Mincell_count_moxi" both give me blanks in the grouped vial view. All fields are of type Integer. I am using labkey 14.1. Is this a bug that may have been fixed in later versions, or did I set something up wrong?

Jen

The sequence numbers show up together with the visit heading in the Study Schedule web part (see attach file). Can I get an advice to fix this?

Anders

Is there a way to create a Message or an email based on upcoming visits/timepoints in a study; as a remainder for the researcher?

Anders

You may have noticed that the 'Date' field (since 14.1) is present in all datasets for a Visit based study. Several users have asked if it were possible to hide this new required field. The desired effect is that the 'Date' field should be hidden when editing or inserting a new record. In response, we have crafted a way to hide this field using a number of different mechanisms involving metadata.

You may configure on a per-dataset, per-study, per-project, or per-server basis to hide the column. At the dataset level, this can be done via XML metadata scoped to that dataset. On a study or project basis this can be done by setting XML metadata scoped to the 'study.studydata' query, either in a module that's enabled for that folder, or via the schema browser. On a server basis you would edit the metadata for the 'study.studydata' query in the /Shared directory which will propagate this metadata to all other folders by default.

Below is sample metadata that will hide the 'Date' column.
<tables xmlns="http://labkey.org/data/xml">
  <table tableName="TestDataset" tableDbType="NOT_IN_DB">
    <columns>
      <column columnName="date">
        <isHidden>true</isHidden>
      </column>
    </columns>
  </table>
</tables>

Hope this helps,
Greg

In order to reduce our ongoing code maintenance workload, we are planning to phase out support for "legacy" study archive formats. These are file formats used by DataFax for dataset and visit map definitions. For many versions, LabKey Server has preferred XML-based formats for this same data. The usage scenario where these legacy formats were being generated by an external system long ago migrated to use the new file formats, and we are not aware of other uses.

We are planning to remove the ability to export studies in the legacy file format as part of 14.3. We will continue to import the legacy formats though. In previous releases, you could export using the DataFax format by choosing "Legacy file format" option in the study or folder export user interface:

https://www.labkey.org/wiki/home/Documentation/page.view?name=importExportStudy

Then, in version 15.1, we plan to remove the ability to import the legacy file formats. In 14.3 and earlier, the server automatically detected the file format option and used the appropriate import parsers.

Please let us know if this plan conflicts with your current usage of the study archive file formats.

Thanks,
Josh

During testing of LabKey 14.1, we have found that we no longer can create query snapshot datasets with more than about 90 columns; we are able to do this in 13.3. Attached is the error output, as well as the SQL of the snapshot. Despite the error, we find that the dataset actually gets created; but it displays no data.

Right now, this is a show-stopper for us upgrading to 14.1.

Please help. Thanks.

Andy Straw
University of Rochester

As far as I can tell, there is no way to control/define the key of a dataset that is created when you copy an assay to study. The dataset created by copy-to-study always seems to have RowId as an additional key column (in addition to ParticipantId and SequenceNum). I understand that this is the safest thing for LabKey code to do, since it can't know if ParticipantId+SequenceNum is unique, and can't know what other field might be the additional key column. However, often for our assays, ParticipantId+SequenceNum IS unique, or there's an additional column we could use to make the dataset rows unique (e.g., a stimulation condition).

Using RowId as an additional key column means that we have to write queries to join datasets that were copied to study from different assays, rather than using Customize View to join them, like we can do with clinical datasets and demomgraphic datasets - even if the data from those assays have the same keys.

Am I missing something, or is there any way to work around this? Or is it reasonable to add a feature to copy-to-study that would allow the user to define the additional key column (or indicate that one is not needed)? Thanks for any info/suggestions you can provide.

Andy

What determines the order in which the levels of a variable string (x axis) appear in boxplot? For example, levels of cohort have a logical order and I would like to set that order in plots. However, depending on the dataset, the ordering by cohort levels varies when using chart wizard or quick chart for boxplots. Sorting a dataset by cohort does not result in a boxplot with ordered cohort levels. Yes, could create R views, but want to enable non-developers to create improved boxplot views.

Using 14.1, when I try to change a dataset's category to something else it looks like it saves but nothing actually changes. Things I've tried:

1. Going through the Manage Dataset button on an individual dataset DataGrid and changing the category text field. It saves without errors but the datset's category value has't changed.

2. Going through Manage -> Manage Datasets -> Change Properties and updating the category on a few datsets. It saves without errors, but the datasets' category values haven't changed.

Is there any other way to update the category for datasets?

Thanks,

Anthony

Hi,
I am trying to set up a microarray pipeline using labkey.
I created a list in labkey containing 28 columns and 45000 rows so I can run R script in labkey using data from this list.
But when I try to use this list it becomes very slow and not very practical to use.
Do you have any advice on it?
Best,
Sasha.

I've noticed that when a user that modifies a record it overwrites the created by user and timestamp on study datasets.

Is this expected behavior?

Hi All,

Here is my situation that I hope the community can help me out with. Lets say I've done two experiments, x and y. I generated two files, x.xls and y.xls. Each of these files contain a list of Gene IDs and their expression. After uploading the two files as lists, is it possible to join these two files and aligning them based upon Gene ID. The end result would be a column of Gene IDs and their expression across the two different experiments.

Hi,

I am new to LabKey and am going through the data management tutorials. I am hoping to use LabKey to store some viral RNA sequence files and export selected sequences (somehow) to an analysis program.

I have created a project and a study, have uploaded numerous files including the LabKey Demo Files. But when I try to import a file from the file repository, nothing happens. The Begin Import, Show Assay Designer, and Cancel buttons don't do anything. I just sit on that page. Also I do get either an "error on page" or "Done" message in the status bar of Internet Explorer. Any thoughts? Thanks.

I can add custom properties to a study, that is, to study.StudyProperties, from the Manage tab, using "Edit Definition". Is there a way to have those additional properties display on the Study Overview web part? Currently, the Investigator, Grant, Description, and ProtocolDocument display, but not other properties.

As folder admin, I can see/edit the other properties by going to the Manage tab and choosing Change Study Properties (or clicking on the pencil icon next to "Study Overview" header on the Overview tab). But other users who are not folder admins do not see the Manage tab or the pencil icon - just the subset of properties displayed on the Overview tab.

Thanks.

Andy Straw
University of Rochester

Consider the following scenario:
- Create a folder of type Study.
- Create a study in the folder.
- Go to Manage tab, select Edit Definition (to add additional properties to the Study)
- Add a Field of type User. Save.
- On Manage tab, select Change Study Properties (with the intent of setting the value of that new User property).
- Study Properties page displays with title, but blank otherwise - none of the properties shows, and so none can be edited.

This seems to happen whenever any Additional Property of a Study is of type User. Having additional properties of other types seems to work fine. I was able to use the Schema Browser to see the study.StudyProperties table, and even set the value of the User property here. But the Change Study Properties link off the Manage tab still displayed a blank page. I had to remove the property of type User to make the problem go away.

Do others see this behavior? Is there something I might be missing? This is using either 12.2 or 12.3.

Andy Straw
University of Rochester

Hi,

I am a new user of LabKey, and first of all, it is an amazing tool that you guys provide to the community. Thanks for that !

About my question, in our study we receive specimens on a daily basis, and we have a temperature logger, within the shipment, to let us know if the specimens were kept at a proper temperature.
These logs are simple CSV files.

How would you advise me to store these CSV file data into LabKey, so that it can be attached to all the specimens that belonged to the corresponding transport.

I hope it makes sense,
looking forward to learning more about LabKey,

best,

Vincent.

When I started setting up a study we only had a production system so all development happened on the production study. Before the study was activated (they started enrolling subjects) I wiped all datasets (no specimens in repository) and cleared all cohort assignments. The study reported 'No participants in study' on the study's main page.

However, the ParticipantVisit table still has rows from the development testing that I had done. Is there a way to clear or recalculate this table? Perhaps based on a summary of StudyData table (which is correct)?


Thanks,

Anthony

I'm looking to get to the data that produces the Study's updateDatasetVisitMapping.view page in my own queries to create a GUI that compares StudyData rows for a participant against what datasets are required for visits. This will enable a study monitor or QA person to quickly see what datasets (which compose an eCRF) are missing.

Looking at the study controller's action updateDatasetVisitMapping, the StudyManager uses a study schema table called 'VisitMap' and has two hard coded SQL queries (VISITMAP_JOIN_BY_VISIT and VISITMAP_JOIN_BY_DATASET) and a method getRequiredMap().

These is perfect for what I want to do, however, the VisitMap table is not available in the schema browser.

Would it be possible to expose this table or at least expose a read only query ( one or both of the two hardcoded in the StudyManager)?


I know there is an study API action called browseStudySchedule.api which populates a Grid view of the study schedule, but the way the data is returned in the resulting JSON is structured very specifically for that Grid and is difficult, but not impossible, to transform for my use case. It would be great to be able to do all transformations and joins in SQL instead of javascript.


Thanks,

Anthony

I'm trying to understand my options for reusing portions of one study in another. We have an existing study folder (StudyA) that we've been using for a couple years. We have built a set of CRFs (about 10-12 forms) that populate about 15 clinical datasets, and use about 15 lists of reference data. The CRFs are wiki/html pages with JavaScript that use/read the lists, and do CRUD operations on the clinical datasets.

Now we're starting a new study (StudyB), and want to reuse the CRFs and associated clinical dataset schemas and lists from StudyA. There are some minor mods that will be necessary (like the code that determines what a valid subject Id is - they're different formats for the two studies), but this shouldn't be much of an issue.

I started down the path of exporting the appropriate parts of StudyA, and then importing them into StudyB. One thing I had to do for StudyB was delete all the records in the datasets that were exported from StudyA. In one case, I deleted the records in the exported tsv file before importing; in other cases, I simply deleted records in StudyB after import, using the LabKey GUI. (Not a big deal, but if there's a way around that, it would be nice.) Now I had StudyB as a copy of StudyA. But certain changes I make to StudyA now have to be manually made to StudyB, if we want them to be the same. We have JavaScript in a shared folder, so that is shared (not copied), but adding a field to a CRF and its dataset would require duplicate work.

Another option I'm looking at is to "factor" the shared parts into a file-based module. If we were starting from scratch, this seems like it might be the way to go. But StudyA is already defined NOT using a module. I'm wondering if I could use the exported study/folder files from StudyA as the starting point for defining a corresponding file-based module. Not sure how far that would get me - for example, are there things that I need that are missing in the exported datasets_metadata.xml and datasets_manifest.xml? Once I create the module, I could use it for StudyB, and then retrofit StudyA to use it (or not). Seems like this is a cleaner way to share wiki pages, JavaScript, schemas across studies/folders, but I'm wondering how much work this will be to do the "factoring" of StudyA into a file-based module.

I also see the concept of Custom Folder Types. Seems like this might be useful on top of a file-based module for additional things that might be shared across StudyA and StudyB, but I'm not sure.

Another option I noticed is "Folder Template". I haven't found clear documentation of how this works. Looks like you export one folder, and then somehow use the export as a template when creating a new folder. I couldn't tell exactly how this works, or what exactly gets used by the new folder from the template. I can experiment to find out, but thought I'd ask here before pursuing that. This would seem to have the same issue as import/export - when you use the template, you get whatever it is at that time; updates to the template don't automatically affect folders created from it before the update. Not sure if that's a good thing or a bad thing.

Any help sorting out these options, and their relative pros and cons would be appreciated.

Andy Straw
University of Rochester

I'm trying to use the enhanced features in 12.2 for exporting and importing a study. When exporting, I check the boxes for "Wikis and their attachments" and "Lists" (and "CRF Datasets"). The exported zip file includes these - I looked. When I import the study, only the datasets get imported, no lists, no wiki pages, and no errors. I was able to get the lists imported separately by unzipping the study zip file, and then re-zipping just the lists contents, and then using "Manage Lists" and "Import List Archive". But I don't know of any way to "import" the wiki pages. I tried to manually copy the contents of the wikis folder via WEBDav to the @wiki sub-folder of the study folder, but I got permission errors, so I assume that's not a valid way to "import" wikis.

I tried doing the export/import both via a zip file to/from my browser, and via the pipeline root as individual files, but both ways behaved the same - neither worked fully.

Is the study import feature not fully working? Am I missing something? Is there a way to "import" just the wikis portion of a study?

Thanks for any help anyone can provide.

Andy Straw
University of Rochester

Hey all,

You probably figured out my problem by the title: I'm trying to reload a study with a zip archive of data files, but the LK interface is reporting: "This file does not appear to be a valid .zip file."

The message is nondescript enough so that I don't know if it is specifically having a problem with the compression or with the contents of the file. Either way, I did my best to conform to the software's expectations. I'm using the CLI `zip` tool on Ubuntu, with the files organized in the archive in the exact same way they are in an export downloaded zip archive, and I've played with the option that (allegedly) forces the archive's compression method to not be zip64. Nothing gets around the aforementioned error.

Any pointers would be appreciated.

Thanks,
Craig

Hey all,

I hope this is the right forum to post this. I'm trying to import some data into the LabKey study module which has a one-to-many relationship, i.e., "duplicate entries by participant ID and sequence ID". (E.g., a subject's medical history. There may be zero entries, or fifteen, or in between, or beyond.) Right now I have it represented as one row per medical history event, but I can reformat if need be.

Is there any way to get the study module to handle this kind of data? (Ideally without forcing it into a denormalized form, since I don't know what the ultimate upper bound will be.)

Thanks,
Craig

Hi all,
I'm looking for some advice on how to set up a database "query" on user-picked files. Given the existing ms1 and ms2 files, I would like to enable my user to pick a number of files. Then, the user should be able to press a button that will execute both a SQL query and a R script to plot a number of graphs.
I reckon that there are a number of ways to do so in LabKey (external module, web part, etc) and I would love to hear your advice on the best way to do it.
I really appreciate your time,
Alex

I am using the power function in a SQL query and it will not show the full decimal points for numerics with negative exponents. I have tried CONVERT (CAST method not recognized) with FLOAT and DOUBLE and it will only show the number as 0.0

Any recommendations on expanding to show as number or scientific notation?

I tried to bring some columns from different table.
So, I went to customize view and looked up the data from "participant visit",
but I couldn't see the datasets what I want.
I have 8 study datasets but only 4 datasets were shown in the columns field.

Noha

I had a simple question of how to change the alignment of axis based labels in a barchart output? i can get it to change in the stand alone R application but am at a loss for how to execute that within labkey.

In an observational study, I'd like to filter a view by
Datetime field and select observations less than 24 hours old.

The customize Grid View interface will let me set up a filter
to select based on a specific date syntax like 2011-02-06, but is it currently
possible to select based on something more dynamic,
roughly like Date - 24 hours, for example?

I wasn't able to find anything about this looking through the
tutorial or docs. Can it be done in the customize view grid?

Dan

I'm sure there's a good reason for this, but why does importing specimen data delete all previous specimen data? Why can't I import specimen data incrementally, adding new sample records to existing sample records?

When I try to enter 1 of my study folders, I get the error message: An error occurred trying to load. Status: /pipeline/Letvin/BCG/BCG 2010- (404). All of the other study folders seem to work fine. This problem occurred after upgrading from 10.1 to 10.3 I checked the mappings for @files and @pipeline and they both seem OK. Any suggestions?

The generic elispot assay design does not have a tab/column for dilution factor. How do I add this?

I am using labkey version 10.2.

One problem I am having is with deleting a row in a study dataset. Whenever I try, I get a NullPointerException:

java.lang.NullPointerException
       at org.labkey.study.controllers.StudyController$DeleteDatasetRowsAction.handlePost(StudyController.java:2393)
       at org.labkey.study.controllers.StudyController$DeleteDatasetRowsAction.handlePost(StudyController.java:2360)
       at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:91)
       at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:75)
       at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:167)

The other problem is I don't see any way to update a particular record in a study dataset. If an entry is wrong or missing a value, how do I change it or add a value to a particular column? I suppose one could delete a row and then add it again (if deleting worked), but that is really ugly.

Any help is appreciated.

There are many pages of documentation relating to pipelines but I still don't seem to be able to work it out...

I have a study that contains a dataset that I imported from a TSV file. What I'd like to do is set up a pipeline so that this file could be imported every time it changes.

I don't see in my study where I can setup and configure the pipeline. I can include the file in 'manage files' but I don't seem to be able to do anything else. In the demo study you can add a pipeline web part. But my study doesn't have a pipeline option in the list of parts I can add.

Can anyone give me a list of the steps I need to go through?

Thanks.

Rick.

Hi. Can anyone help me set up a SQL Server database as an external data source? We have LabKey running against a PostgreSQL database and can successfully access external SAS data sets. However we'd like to use LabKey to report on data from a SQL Server database. The instructions in the documentation seem to relate to replacing Postgres with SQL server, which is not what we want.

Do we need to install the BigIron module as the documentation implies?

What should I put for the data source element in labkey.xml?

Thanks.

Rick.

Hello, I would like to test out the Nab Module and was curious what the data file template looks like. it only states that "The NAb data file is a specially formatted Excel 1997-2003 file with a .xls extension." but does not offer a glimpse of it.

any suggestions?

aaron

i was curious about the missing values indicator if i was going to be undertaking sql scripts when dataset is uploaded. is there an R equivalent to na.rm=T in sql to be able to use the data in tabulation. thanks for any information.

Hi,

Is there a way to clone a whole study with datasets, cohorts, visits, lists, etc.? We have multiple studies with very similar settings and this would make support much easier.

Thanks,
Tamas

We have a study the with a hierarchy, Experiment> group> mouse. Each experiment has a different number of groups.
On the data input forms, when the user selects an Experiment they would like the group selection to change to the number of groups appropriate for that experiment. Or, could validation be implemented that related the experiment field to the group field. If each experiment were a study then cohorts could be used for the groups but the user wants everything in one study. Any features that can help with this? We're using 9.3.
Thanks,
Bill

users can't see R or advanced view in the create view list even though they are in a group that has project and folder admin permissions and study edit all permissions.

Is there a link from assay data to the specimen that was used in the specimen repository. For example, using the tutorial data and the Microarray assay, is there a way to determine and view specimen used for each run?

If I select an assay from the miccroarray dataset and select "View Specimens" it gives an empty list with the message:
This view is displaying specimens only from particpant(s) 249320489 at visit "2.0081203E7"

In study datasets, is there a way to set permissions on single fields to read-only or hidden while allowing the others to be editable?
Thanks,
Bill

So I've just installed Labkey 9.2 and am attempting to import some data into a study. I am on the 'define dataset from file' page and have selected a tab delimeted file. The problem is that I get lots of 'datatype error for field' messages.I believe the problem is caused by text in otherwise numeric fields. I have text such as UNK to represent missing values.

Can anyone tell me how the missing values feature of Labkey works? I assumed tah if I defined the appropriate codes as missing value indicators they would import ok, but this does not seem to be the case.

Thanks

Rick Watts
Women & Children's Health Research Institute
Edmonton, Alberta.

I'm trying to set up the demo tutorial and I don't think I have the correct demo files.
I downloaded them from https://www.labkey.org/wiki/home/Documentation/page.view?name=setupDemoStudy > Demo files for study
For example the tutorial says to import Demographics.xls but the set I found has two files:
Demographics-- Dataset.xls
Demographics-- Schema.xls

The Demographics-- Dataset.xls kinda works but it doesn't have a date column.

Thanks,
Bill

Hi there,

I created a custom list in 9.2 that had 36 fields of types string, multiline, DateTime, and Integer. The list appeared to create fine, but when I went back to edit the fields, I got the following error:

ERROR: There was an error processing the request. (Error type: org.apache.commons.beanutils.ConversionException)

Any ideas what could be causing this? I'm attaching the log file to this message.

Any help would be greatly appreciated!

Thanks,

dave

Hi,

I am new to LabKey and I need to upload some illumina microarray data to our server. I have a test MAGE-ML data file. I have been able to upload the test MAGE-ML data file to the pipeline root on our LabKey box. From inside LabKey I cannot see the data file when I press the "Process and Import Data Button" or the "Browse for MAGE-ML files" button. I have admin rights in LabKey. I am struggling as to what is needed for the pre-requisites to get the ball rolling on this import.

If there is a microarray upload tutorial with a few screen shots and a test MAGE-ML file that would be very helpful. I seem to see very little in the documentation about importing microarray data. Any help or pointers at all on this would be most appreciated.

Cheers,
Roy

LabKey on CentOS linux.

I'm trying to create a dateTime field for time only.
I entered the format "hh aa" to represent, for example, 04 pm.
The error message is - Could not convert value: 04 pm.
Can you please give me an example of how to format a time correctly and tell me why this is not working?
Thanks,
Bill

Can you direct me to more information about how the list web part is used in an observational study. Is some of our data sets a field will have a small list of possible entries and these need to be entered in a consistent manner(like a select list on a form). Can lists be used in this way?

Thanks,
Bill

Can the forms for manual single entry in to a dataset be modified easily? For example, can field validation be added to the form; can fields become multi-select boxes to limit choices.
Thanks,
Bill

On the Study overview page (https://www.labkey.org/wiki/home/Documentation/page.view?name=evaluateStudyOverview) there is a link to:

Introductory Video

An introductory video demonstrating how use LabKey's Study Module is available on the SCHARP Atlas site:

Atlas Overview<a href="https://atlas.scharp.org/cpas/login/Support/login.view?URI=https://atlas.scharp.org/cpas/Project/Support/begin.view%3F"/>

but the link goes to a login page. Is there a guest login available?

Thanks,
Bill

After completing the demo I am wondering if there are some best practices for maintaining the participant id and sequence number. How are the excel spread sheets usually created? Extracted from another database?

Thanks,
Bill

I'm going through the Study tutorial.
I have started the "Create a Dataset and Define its Schema" section.

I can't find the checkbox described in this step:
Click the Import schema from spreadsheet checkbox under the "Dataset Schema" section.

Have made an error in my setup or has this changed? Using 8.2. Screen capture attached.

Thanks,
Bill

When I ran a simple R command at R view bulider, I got the following error message;
"An error occurred rendering this view, you may not have permission to view it"

I installed labkey 8.1 on windows xp (C:\Program Files\LabKey Server)

How can I fix this problem? I attached the pictures of the configuration.
Thanks.

I am trying to print labkey.data in a html table format using R view.
I need to run for-loop in R view html, because the length of the data is not deteremined.
e,g., I want to print all date samples used according to a study ID.
for (var aNum = 0; aNum <= length(labkey.data$studyID); aNum++)
              document.write(labkey.data$dateSampleUsage);


Is it possible to pass R varilabe to html?
html does not support variables.
Does R view support java script?



txt <- paste(
"<TABLE border='1'><CAPTION><EM>A test table RNA Extraction Worksheet </EM></CAPTION>
<TR><TD>Patient: ",labkey.data$studyID[1],"<TD>Sample Day: ", labkey.data$sampleDate[1], "<TD>Extract Day: ", labkey.data$extractionDate[1], "<TD>Performed by: ", labkey.data$userInitials[1], "<TR><TD>Protocol: ", labkey.data$protocol[1], "<TD>Volume: ", labkey.data$voluL[1], "<TD>A260: ", labkey.data$a260[1],

"<TR><TD><img src='http://cpas01.sbri.org/files/Morogoro_RNA/bioan.jpg' HEIGHT=327 WIDTH=291>", "<TD>volLeft: ", labkey.data$volLeft[i],


 "</TABLE>",
"<SCRIPT LANGUAGE='JavaScript'>
    <!--
    document.write('<H2>Multiplication table for 4</H2>');
     
    for (var aNum = 0; aNum <= length(labkey.data$studyID); aNum++)
    {
      document.write('4 X ',aNum,' = ',4*aNum,'<BR>');
    }
    //-->
</SCRIPT>")

I am working on R report view, because I need to add jpg pictures into the formatted report (see attached file; Amplification.tif).
My plan was using rimage and plot to generate a pdf file (see labkeyl_pdf.pdf).

I could not insert a jpg file into the pdf file yet, since I could not install 'rimage' package.
for example;

library(rimage)
datalogo<-read.jpeg("/usr/local/labkey/datasets/morogoro_rna/bioan.jpg")
plot.imagematrix(datalogo)

Is there better way to do this with Labkey ?

Thanks.

I am trying to install R packages for Labkey.
I am an admin for Labkey, but not an server system admin.

I installed one package using R package local installation at a console;
R CMD INSTALL pixmap_0.4-7.tar.gz

I could use that library in the regular R window, but not in Labkey R script view.

I think the installed R packages are available only to me, because it's the local installation; I can install R packages in one of my folders. I can't install R packages in '~R/lib' because I don't have writing access to that folder.

Should the server system administrator install R packages (~R/lib) for Labkey?

Thanks.

I followed the path below to go to the R script of the query 'JC' that I joined all tables in labkey
Manage Reports and Views -> new grid view -> Modify Dataset List (Advanced) -> 'JC' run -> R script veiw

I placed query tab in front of the project page, but it does not show the R script view I made.


I attached two image files;
labkeyRq.JPG shows the R script view

labkeyRq1.JPG does not show the R script view.

Can I place the query 'JC' with the R script view?

I know I can directly place R script view using 'manange report', but I need to show all data to users first and then let them select one ID and then generate R report for that specific ID.

Thanks.

I joined all tables in Labkey.
Now, I am trying to generate R report view into a pdf file.
I attached the report view done by hand for examples.
Unfortunately, I do not know much about R.
Is it possible to generate such reports using R ?

Can I insert a image file (generated by a lab equipment) into each report.
   Or can I add a link to a file using labkey?


Thanks.

I tried to query two tables Extracted_RNA and Extracted_RNA_Use_Log in Labkey
I used the following query at
study queries >

SELECT Extracted_RNA.ParticipantId,
Extracted_RNA.ExtractionID,
Extracted_RNA.SampleBarcode,
Extracted_RNA.BioanalyzerResultsPDF,
Extracted_RNA.A320,
Extracted_RNA.Notes,
Extracted_RNA.ParticipantVisit.Extracted_RNA_Use_Log.PurposeofUse
FROM Extracted_RNA

It did not work

Query 'RNA_Extraction_Worksheet' has errors
Error on line 25:Unknown field Extracted_RNA.ParticipantVisit.Extracted_RNA_Use_Log.PurposeofUse

But there was the field 'PurposeofUse'.
I attached the screen shot, datasets, and schemas.
I think Labkey could not find the field because 'Extracted_RNA_Use_Log' had an additional key 'ExtractionUseID'
Also Labkey did not display 'Extracted_RNA_Use_Log' under participantId in Customize Grid View


Is it right? How can I join or query datasets with additional keys?

I opened one study dataset and went to Customize Grid View
I could not see other datasets after clicked participant visit.
Was it because I added additional key to other datasets's schema?

I saw datasets without any addtional key under participant visit.

Thanks.

Wonjong.

Hi Matt and Sarah,
 
I've been playing around on our server and trying to set up a simple study that is already in progress as a means of figuring out this whole system. It is Barouch\07-06. I noticed a few things that need tweaking for animal studies. I know that there are changes in 2.3 as far as animal studies, so I realize that these items may already be improved in 2.3. Here goes:
 
1) In the study protocol definition under assays when you define a new assay the material required section does not allow you to add to the drop down menus. Right now I have the requirements set as 0.5 ml PBMC, but I'd really like it to say something like 0.5ml lysed whole blood.
 
2) In the assay schedule it would be nice to be able to either import a schedule or be able to define multiple timepoints. In animal studies we have many more timepoints than in human studies. I might have seen some way to import this, but I have no idea how I got there ~or even if that's what it really was.
 
I hope to add the flow areas next week. It's really simple analysis that won't need any compensation, very few gate adjustments, and well defined results that we're interested in.
 
Thanks,
 
Michelle

The 2.0 documentation describes a pipeline configuration file that contains a set of property/value pairs, and that this configuration file for dataset import is named with the .dataset extension. It is unclear to me from the documentation, however, where this configuration file should be placed. Perhaps I'm missing something obvious, but could someone tell me
where the .dataset file should be placed? Thank you.

Dan

Whenever I navigate to Manage Study > Manage Visits > [edit] (any of the defined visits)
the values in the drop-down field for the Associated Datasets are not completely correct.

If the value has been set to "optional" or "required" it is displayed correctly. If
however the value has been set to "not_associated", the dropdown has the value for
"optional" selected. It is really a minor issue that just makes it easy to screw up
your visits if you are not careful.

All of my visits and datasets were defined manually in the GUI.
I an running the source from the trunk checked out on 3-12 and postgres 8.1.6.

It would be very handy to have the ability to add custom fields to the study specimen object. Are there any plans afoot to add this functionality?