I ran independently 2 differential expression experiments using DESeq: . CONDITION_1 vs REFERENCE . CONDITION_2 vs REFERENCE
(REFERENCE is the same for the 2 CONDITIONS)
I got 2 tables like below showing the differentially expressed genes between my sample and the REF (1 table per CONDITION):
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval ENSG00000000005 3.5 1 6 6 2.584962501 0.445151971 ENSG00000000419 14.5 15 14 0.933333333 -0.099535674 1
Within each condition:
(1) Does a positive log2FoldChange means that the gene in the sample is over-expressed compared to the REF?
(and a negative log2FoldChange for down-expression?)
Between 2 conditions:
(2) To know which gene shows the largest difference in expression between CONDITION_1 and CONDITION_2, would it be correct to simply make the difference of the 2 respective log2FoldChange?
(i.e. log2FoldChange_CONDITION_1 - log2FoldChange_CONDITION_2)
Or could we do a ratio of the 2 p-values instead?