GSEA time series analysis - cls file format?
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3 months ago
garfield320 ▴ 10

Hello, I'm trying to do an enrichment analysis of proteins collected over time (days = 1, 2, 3, 4) using GSEA, and was confused about the format of cls file that I need to provide.

I found that for categorical labels, I basically need to assign each column of my data to each phenotype, like below:

#Firstday Secondday Thirdday Fourthday
f f f f s s s s t t t t o o o o


But for continuous labels, the examples I were able to found looked like below:

#numeric
#IncreasingProfle
1 2 3 4


I tried loading this file and running the analysis, which worked without any errors, but I was confused if GSEA was going to only use the first four columns of my entire dataset. Is my understanding correct that I'll need to use a cls file like below instead if I want to make sure all of the columns in my dataset are assigned correct phenotypes?

#numeric
#IncreasingProfle
1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4

GSEA cls • 102 views