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best way to analyze a subset of DE genes

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.

rna-seq deseq expression gene
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written by Lila M Lila M

How reliable is the positive control, so what experiment was done that this gene is truely DE?

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written by ATpoint ATpoint

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

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written by Lila M Lila M

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.

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written by ATpoint ATpoint

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?

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written by Lila M Lila M

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