I was able to retrieve the counts from my RNAseq analysis via Cuffdiff so as to compare with the FPKM values
Please tell me what the decimal points in counts correspond to, because as is, i cannot make much sense of the data
I read in some forums that the value for Counts should be the same as FPKM if your analysis is single-paired as mine - but that is not the case for my data. Should that be the case, what do you think went wrong in my analysis, and what should I do to fix it?
When I compare the data from FPKM vs counts, even if the values differer, the outcome is usually the same in regards to deferential regulation e.g if my Test value shows up-regulation in regards to the WT, 99% of the time I will also see that it is up-regulated when I'm looking at counts. So why don't all data correlate? Also in a couple of cases I got genes that had zero counts but had a value when it came to FPKM. How is that possible?