More results when prefiltering in DESeq2
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10 months ago
Stella • 0

Hello community,

I have been using deseq2 for a while now and as is written in the tutorial, prefiltering is only necessary because of computational power since the results function applies the appropriate filtering. I have noticed that doing my analysis both ways, without prefiltering or applying a minimal filtering of 10 counts per row, sometimes I can get a few more genes in the prefiltering scenario. And visualizing them in a heatmap those extra genes have a similar image with the rest, that came out in both cases. So visually, the extra genes do seem differentially expressed to me.

I am a bit troubled on which scenario to trust more. Or if both of them are equally correct and it's just a statistical matter of the amount of genes that you give to the tool and how that affects the padj values of the results.

Many thanks in advance!

deseq2 prefiltering • 434 views
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the assumption of removing line with < 10 counts is that the low counts gene could be background noise.

In general, filtering gives you results with less sensitivity but more specificity(less false positive) and non-filtering means more sensitivity but less specificity (more false positive).

So the answer of your question depends on what you want in the end.

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Ok!Many thanks for your answers, it is clear!

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