GSEA time series analysis - cls file format?
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
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