Data formats

Expression data formats

1. <a href="../../../doc/data_formats.html#gct">GCT: Gene Cluster Text file format (*.gct)</a>
2. <a href="../../../doc/data_formats.html#res">RES: ExpRESsion (with P and A calls) file format (*.res)</a>
3. <a href="../../../doc/data_formats.html#pcl">PCL: Stanford cDNA file format (*.pcl)</a>

Phenotype data formats

1. <a href="../../../doc/data_formats.html#cls">CLS: Categorical (e.g tumor vs normal) class file format (*.cls)</a>
2. <a href="../../../doc/data_formats.html#cls2">CLS: Continuous (e.g time-series or gene profile) file format (*.cls)</a>

Gene set database formats

1. <a href="../../../doc/data_formats.html#gmx">GMX: Gene MatriX file format (*.gmx)</a>
2. <a href="../../../doc/data_formats.html#gmt">GMT: Gene Matrix Transposed file format (*.gmt)</a>
3. <a href="../../../doc/data_formats.html#grp">GRP: Gene set file format (*.grp)</a>
4. <a href="../../../doc/data_formats.html#mdb">MDB: Molecular signature database file format (*.mdb)</a>

Microarray annotation formats

1. <a href="../../../doc/data_formats.html#chip">CHIP: Chip file format (*.chip)</a>
2. <a href="../../../doc/data_formats.html#map">MAP: Chip mapping file format (*.map)</a>

Ranked gene lists

1. <a href="../../../doc/data_formats.html#rnk">RNK: Ranked list file format (*.rnk)</a>

Note: The GCT & RES expression formats supported by GSEA are identical to those supported by GenePattern. Some description is duplicated here - the GenePattern website has more documentation on file formats.

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<a name="gct">GCT File Format</a>

The GCT format is a tab delimited file format that is organized as follows
<img alt="GCT format snapshot" src="../../../images/gct_format_snapshot.png" />