LRT, pairwise comparisons and p-value adjustment
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boczniak767 ▴ 740
@maciej-jonczyk-3945
Last seen 8 days ago
Poland

Hi,

this question is related to pariwise comparisons of expression profiles using LRT in DESeq2. Question is related to my previous question LRT, more than two conditions and pairwise comparisons

I have four maize lines and 12 time points. I'd like to check if expression profiles are different. I know I can do LRT for two groups only. The result table gives adjusted p-value.

However if I make six such tests (LRT procedures) should I adjust p-value using total number of comparisons from all pairwise trests (LRT procedures)?

DESeq2 • 168 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

The convention is to adjust only within comparisons. But as the analyst, that's your call.

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