MAGE-TAB format for raw and processed data matrix

Data matrix format

This format allows each data point in the file to be mapped to a particular assay in the experiment, and to a particular probe/probe set in the array design file of your experiment. For the mapping to work smoothly, each matrix file should contain data from assays on a single array design (i.e if you use multiple array designs in your experiment, mutliple matrix files will be needed), and the column/row headings and the order of columns are strictly controlled:

Column/row headings:

The first header line of a matrix file, Hybridization REF, allows assay-mapping via assay names. The second header row lists the "quantitation types" for each column (i.e. the type of measurement recorded in the column, e.g. log2 ratio). Finally, the first column, Reporter REF is used to map the data rows to probe identifiers from the array design file.

Measurements calculated from multiple assays:

Measurements such as Log2 fold-changes are often calculated from more than one assay (e.g. for every given gene, calculate the average of 3 knockout samples vs the average of 3 wild-type controls). In that case, you can put down multiple assay names per column, with the assay names separated by semi-colons:

Hybridization REF Hyb1;Hyb2;Hyb3 Hyb4;Hyb5;Hyb6
Reporter REF log2 FC log2 FC

Order of data columns:

The format requires an ordered and regular organization of the columns: first by assay, and then by quantitation type:

Correct

Hybridization REF Hyb1 Hyb1 Hyb2 Hyb2
Reporter REF log2 FC p-value log2 FC p-value

Wrong

Hybridization REF Hyb1 Hyb2 Hyb1 Hyb2
Reporter REF log2 FC log2 FC p-value p-value

Example non-Affymetrix data matrix

In this example, four of the six assays are being mapped to log2 ratio values in the matrix file. Each row of data is mapped to a Reporter Name defined in the array design file, in this case, A-AGIL-6.

Assay Name nodes in SDRF:

Assay Name
Sample 1:Cy3
Sample 2:Cy3
Sample 3:Cy3
Sample 4:Cy3

Non-Affymetrix data matrix:

Hybridization REF Sample 1:Cy3;Sample 2:Cy3 Sample 3:Cy3;Sample 4:Cy3
Reporter REF log2 ratio log2 ratio
A_42_P834147 4.2 2.6
A_43_P19480 1.9 1.3
A_42_P495989 5.3 9.8

Example Affymetrix data matrix

In this example, two of the six assays are being mapped to data with two different quantitation types (CELIntensity, CELStdev). Each row of data is mapped to a CompositeElement Name (because each Affymetrix probe set is made up of a number of probes), defined in the array design file, in this case, A-AFFY-44.

Assay Name nodes in SDRF:

Assay Name
Sample 1:biotin
Sample 2:biotin

Affymetrix data matrix:

Hybridization REF Sample 1:biotin Sample 1:biotin Sample 2:biotin Sample 2:biotin
CompositeElement REF CELIntensity CELStdev CELIntensity CELStdev
AFFX_ThrX-M_at 142.1 2.6 199.1 6.5
20050_at 70.4 1.3 88.3 4.7
20051_at 227.3 9.8 213.2 3.5