IRFinder Diff Interpretation

[mguaita]

Dear Claudio,

I am finding trouble to interpret the log2FoldChange results of Deseq2 as passed by IRFinder Diff.

IRFinder Diff -g:P1 file_paths -g:Ctrol file_paths -v

Terminal verbose: The given groups are:

• Group P1: 34 samples
• Group Ctrol: 12 samples log.out file: [1] "Intercept" "Condition_P1_vs_Ctrol"
  [3] "ConditionCtrol.IRFinderIR" "ConditionP1.IRFinderIR"

Here "Ctrol" is the reference level and Fold Change is defined as "P1" compaired with "Ctrol", is it right? or is it using P1 as the reference level instead of the control group?

Thank you very much!

[CloXD]

Hello Maria, that's correct, the FC refers to the first condition respect to the second. If you have some doubts, you can check one event having high FC and low p-value and see if the distribution of the IR ratio is coherent with the fold change. Cheers, Claudio