I have five experimental groups (A, B, C, D, and E; 3-6 bioreps each) that I want to compare to each other and a control (Y; 3 bioreps) using DESeq.

When I run DESeq is it better to use a count table that includes A, B, C, D, E, and Y, then run each comparison, or is it better to make a count table for each comparison (ie: a table for A and Y, another table for B and Y, another table for A and B, etc.) and end up with ~15 different count tables?

I ask because I end up with different lists of significantly changed loci depending on how I run the analysis and I'm not sure which is more 'correct.'

When I run DESeq is it better to use a count table that includes A, B, C, D, E, and Y, then run each comparison, or is it better to make a count table for each comparison (ie: a table for A and Y, another table for B and Y, another table for A and B, etc.) and end up with ~15 different count tables?

I ask because I end up with different lists of significantly changed loci depending on how I run the analysis and I'm not sure which is more 'correct.'

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