My question is related to a DESeq2 output where apparently log2 fold-changes are wrongly calculated.
Let me, please, explain the case with one gene result:
Raw counts for that gene (HTSeq-count):
Ctrl 2200, Treatment 2097
Normalised counts by DESeq2:
|Ctrl 2215.3490440231||Treatment 2082.4709372308|
Log2(treatment/control) from differential expression test
I expected the log2fc to be -0.0892376619
I must say that this test is done without replicates, only one control sample vs its corresponding treament sample. Could this affect in some way??
When I perform the same test with 3 controls and 3 treatments, used as replicates for the two conditions, the log2(fc) are correctly calculated.
**The control and treatment samples shown here participate also as one of these 3 replicates for each group.
thanks very much !