Question: DEXSeq With Reduced Annotations
gravatar for sumeet460
5 weeks ago by
sumeet4600 wrote:

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

ADD COMMENTlink written 5 weeks ago by sumeet4600

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.

ADD REPLYlink written 5 weeks ago by chris86380

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Alejandro Reyes1.6k
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