DEXSeq With Reduced Annotations
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sumeet460 • 0
@sumeet460-15155
Last seen 3.7 years ago

I have a question about using DEXSeq on a reduced annotation set. I have a set of genes that I used to filter the flattened gtf / gff file, and used this file to count reads only in those exons.

My question is how to interpret p-value, q-value, and log2 fold change in this context.

Should I interpret a q-value < 0.05 as being a bit inflated since there are many fewer exons being tested? Is there anything else about the resulting output that will be affected in a way that changes biological interpretation?

thanks, Sumeet

dexseq reduced annotation set • 484 views
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Can't see why that would matter unless you have pre-selected those genes due to a prior statistical test and therefore would be biasing your results.

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I agree. If your filters are independent under the null hypothesis, your analysis should be fine.

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