I have three cells with many genes (for example one of my data is as follows)
Gene Name Drug1 Drug2 Drug3
1007_s_at -0.2815 -0.2032 -0.2539
1053_at -0.0113 0.0285 -0.0675
117_at -0.0448 -0.136 -0.2189
121_at -0.081 0.1412 0.0464
Based on my search I found I should obtain t-test, then p-value etc. There are many functions in r as well as Java which can be used for GSEA. However, I am stuck at the first step , how to prepare the data set and then how to analysis them? I don't mind to analysis with any software available , just can you please one of you help me how to do it ?
I am looking forward to hearing from you