The expression matrix assay ties expression-level information to sample and feature/probe information. After appropriate files are loaded into the system, users can explore microarray results by building queries and visualizations based on feature/probe properties (such as genes) and sample properties.

Expression data may be manually extracted from Gene Expression Omnibus (GEO), transformed, and imported to LabKey Server.

Tutorial steps:

• Review File Formats
• Set Up the Folder
• Define Sample Type
• Import Sample Information
• Add Feature Annotation Set
• Create an Expression Matrix Assay Design
• Import a Run
• View Run Results

• Metadata about features/probes (typically at the plate level)
• Sample information
• Actual expression data (often called a "series matrix" file)

Review File Formats

In order to use the assay, you will need three sets of data: a run file, a sample type, and a feature annotation file.

The run file will have one column for probe ids (ID_REF) and a variable number of columns named after a sample found in your sample type. The ID_REF column in the run file will contain probe ids that will be found in your feature annotation file, under the Probe_ID column. All of the other columns in your run file will be named after samples, which must be found in your sample type.

In order to import your run data, you must first import your sample type and your feature annotation set. Your run import will fail if we are unable to find a match for your ID_REF value for a sample in your sample type. If you don't have current files, you can use these small example files:

• sample_expression_matrix.tsv
• sample_feature_annotation_set.txt
• series_matrix.tsv

Set Up the Folder

Define Sample Type

• Click New Sample Type.
• On the Create Sample Type page, name your sample type. Here we use ExpressionMatrixSamples.
• In the Naming Pattern field, enter the following, which means use the ID_REF column as the unique identifier for samples:

  ${ID_REF}

• Click the Fields section to open it.
• Click Manually Define Fields.
• Use Add Field to create all the fields that will match your spreadsheet.
• Three built in fields, Name, Description, and Flag, all of type Text, are always created and should not be included on this list.
• For each field enter a name without spaces and select a data type. For our sample, enter:
• ID_REF - Text
• SampleA - Integer
• SampleB - Integer

• Click Save.

Import Sample Information

Now that you have created the new sample type, you will see the name in the Sample Types web part.

• Click ExpressionMatrixSamples to open it.
• Click Import More Samples.
• Into the Data area, paste in a TSV of all your samples (or you can click Upload file... and upload the file directly).
• The file sample_expression_matrix.tsv you downloaded contains this data:

• Click Submit.

Add Feature Annotation Set

Create an Expression Matrix Assay Design

Import a Run

Runs will be in the TSV format and have a variable number of columns.

• The first column will always be ID_REF, which will contain a probe id that matches the Probe_ID column from your feature annotation set.
• The rest of the columns will be for samples from your imported sample type (ExpressionMatrixSamples).

ID_REF GSM280331 GSM280332 GSM280333 GSM280334 GSM280335 GSM280336 GSM280337 GSM280338 ...

An example of row data:

1007_s_at 7.1722616266753 7.3191207236008 7.32161337343459 7.31420082996567 7.13913363545954 ...

To import a run:

View Run Results

After the run is imported, to view the results:

There is also an alternative view of the run data, which is pivoted to have a column for each sample and a row for each probe id. To view the data as a pivoted grid:

Related Topics

• Create Sample Type