DESeq2: Less significant genes if more samples added?
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michael • 0
@michael-21908
Last seen 4.9 years ago

I guess this is not only specific to DESeq2 but also to other methods like edgeR, etc.

I do not have any data for this or any code. It is more of a general question.

Assume you have the following setup: - 5 Control samples - 5 Treated samples

Now, also assume that we have a rather "low effect" from the treatment on the expression of genes. Would you be surprised if you find more sign. DE expressed genes if you take only 4 treatment samples compared taking all of them (5 treatment samples). Or different: Is it a common effect to get less sign. DE genes if you have a higher sample size? Again, especially if you do not have strong effects from the treatment.

deseq2 • 386 views
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@mikelove
Last seen 17 hours ago
United States

You would generally expect more rejections of non null genes with higher sample size. However, its easy to imagine situations where removing a particular sample or set of samples (eg failed samples) where you recover more signal without them.

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