GSEA phenotype label file and expression data relation

Question

[biology_inform]

Hi all, I am pretty new in GSEA and so I have a basic question about it. In .cls file (which contains phenotype labels), the third line contains labels according to phenotype. Their phenotypic order must be same with the order at expression data right? This is how they match i think.

To exemplify, I have a data that contains 10 samples but they are differentiated according to p53 expression. So the samples phenotypic order is like below

Low High Low Low Low High High High Low High

So the .cls file should be like this or not;

10 2 1
Low High
0 1 0 0 0 1 1 1 0 1

Thanks in advance

Answer 1

[iraun]

Hi! Yes that is correct. Sometimes to simplify the writing of third line in the .cls file, one can reorganize the expression data file, and group the different classes together, like, all "Low" samples first, and then all the "High", so that the risk of "human error" decreases.