前面文章介绍了R GSEA（Gene Set Enrichment Analysis）快速入门，当我们用GSEA软件做数据分析的时候，对其文件格式却知之甚少，本文根据官方的介绍做了汇总整理。
软件下载：
| GSEA v4.1.0 Mac App | Download and unzip the Mac App Archive then double-click the GSEA application to run it. You can move the app to the Applications folder or anywhere else. | download GSEA_4.1.0.app.zip |
|---|---|---|
| GSEA v4.1.0 for Windows | Download and run the installer. A GSEA shortcut will be created on the Desktop; double-click it to run the application. 64-bit Windows is required | download GSEA_Win_4.1.0-installer.exe |
| GSEA v4.1.0 for Linux | Download and unzip the Archive. See the included readme.txt for further instructions. 64-bit Linux is required | download GSEA_Linux_4.1.0.zip |
| GSEA v4.1.0 for the command line (all platforms) | Download and unzip the Archive. See the included readme.txt for further instructions. Requires separate Java 11 installation. | download GSEA_4.1.0.zip |
| GSEA v4.1.0 Java Web Start (all platforms) | Launches the GSEA desktop application from the web. Requires separate Java 8 installation. Please use a configuration smaller than your computer’s total memory. This option will be removed in a future release. | Launch with 1GB (for 32 or 64-bit Java) 2GB (for 64-bit Java only) 4GB (for 64-bit Java only) 8GB (for 64-bit Java only) |
主要涉及5类文件格式：
1）表达矩阵文件
GCT文件（比较常用）: Gene Cluster Text file format (*.gct)
RES文件: ExpRESsion (with P and A calls) file format (*.res)
PCL文件: Stanford cDNA file format (*.pcl)
TXT文件（ 推荐 ）: Text file format for expression dataset (*.txt)
注意：第一列和第二列表头必须为NAME、 Description
2）表型文件
CLS文件: Categorical (e.g tumor vs normal) class file format (*.cls)
3）基因集数据库文件
GMX文件: Gene MatriX file format (*.gmx)
GMT文件: Gene Matrix Transposed file format (*.gmt)
GRP文件: Gene set file format (*.grp)
XML文件: Molecular signature database file format (msigdb_*.xml)
4）芯片注释文件（现在芯片使用相对较少）
CHIP文件: Chip file format (*.chip)
5）基因的排名文件（输出结果会包含）
RNK文件: Ranked list file format (*.rnk)
当你了解了GSEA涉及的各种文件后，使用GSEA软件将会更加容易。
参考资料：
1.http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
2.http://www.broadinstitute.org/gsea/
