LabKey Server provides support for microarray data with two separate but related approaches. In the first, the server tracks imported data files (both Agilent and Affymetrix are supported) and associates them with sample information and other metadata. In the second, the server imports normalized expression-level data and makes it available for downstream querying and reporting.
Microarray Data File, Sample, and Other Metadata Tracking
The Microarray module supports workflows for both Agilent and Affymetrix. In both cases, the raw content of the data files is not imported into the LabKey Server database. The files remain available for download and analysis in R other other tools. Administrators can define the exact set of fields tracked for each sample associated with a microarray run.
For Agilent, the server automates running the Feature Extractor software on the instrument generated TIFF file, and then associates the resulting MAGE-ML data file, along with a PDF QC report, a JPEG thumbnail, and other outputs with sample information and customizable, user-entered run-level metadata.Tutorial: Microarray Assay Tutorial
- Demonstrates import of Agilent MAGE-ML files.
For Affymetrix, the server expects to receive an Excel file with sample and file information, along with the .cel files generated by the instrument. The implementation has been used successfully with the GeneTitan instrument. No tutorial is provided for working with Affymetrix data.
Microarray Expression Matrix Import
The "Expression Matrix" assay imports a normalized expression and associates each value with a sample and its feature or probe from the array. Administrators upload metadata about the probes being used, with their associated gene information. Users can upload sample information (including whatever fields might be of interest), along with expression data. Since the full expression data is imported, users can filter and view data based on genes or samples of interest. Additionally, the data is available to hand off to R, LabKey Server's standard visualization tools, and more.Tutorial: Expression Matrix Assay Tutorial