Hello, I recently used DEseq2 to compare featureCounts output from 9 samples: 3 in each of 3 factor levels:
Factor: Day
Level 1: Day1 (samples 1, 2, 3)
Level 2: Day2 (samples 4, 5, 6)
Level 3 Day3 (samples 7, 8, 9)
When run through DEseq2, the output is one data file and one summary pdf (with the pca plots, histograms, etc). The data file has a lists of genes, with all the normal output: log2(FC), p-value, p-adj, Wald, STDerror, etc.
My question is: What do the fold changes and p-values mean? I suppose I would expect 3 different fold change values (ie 2 vs 1, 3 vs 1, 3 vs 2) but instead just get one value for each gene across the 3 factor levels. Did I do something wrong in the settings?