I have the excel file generated from Cuffdiff output for genes with the following columns
Gene, locus, sample_1, sample_2, status, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant
Casp1, chr9:5298516-5307281, MUT, WT, OK, 123.019, 0.671358, -7.51758, 6.17607, 6.57E-10, 6.36E-07, yes
As per the excel file, sample_1 is Mutant and sample_2 is Wildtype. Log2(fold_change) is calculated as log2(sample_2/sample_1) --> log2(0.671358/123.019) is -7.51758 .
I thought it should be log2(final/initial), isn't it?
What is the difference between log2(Mutant/Wildtype) or log2(Wildtype/Mutant)?
How to show the fold change (like 4-fold, 5-fold change) in heatmap?