Entering edit mode
3.1 years ago
Lila M
★
1.2k
Hi all,
I have the RNAseq data for an experiment, with data under two condition. I've performed the typical DE analysis using DESeq in R. On the other hand, I have a positive control genes from the lab, but unfortunately, those genes are not DE in my analysis. So now, I'm wondering if there is any way or a different analysis that I can do to see if those genes have any effect at all in both conditions or if I should think in other strategy.
Thank you very much.
How reliable is the positive control, so what experiment was done that this gene is truely DE?
It is an in-house method who is very reliable actually (can't explain so far). It has not be tested as DE in lab, but the genes have an effect
Maybe you should sort out with them whether this is, on a transcriptional level, really a good positive control, and decently expressed so you have the statistical power to call it DE. With the given information there is probably not much to add at this point.
because there is no other kind of analysis than can be done with the RNA seq apart from DE to test this kind of differences, right?