Pre-Filtering and Independent Filtering DESeq2

Question

[turcoa1]

Hello,

Quick question regarding independent filtering and prefiltering. In my differential expression analysis pipeline, I filter out genes based on a quantile threshold prior to running DESeq2. My question is, since I already did this prefiltering step prior to running DESeq2, should I turn the option for independent filtering off when I run the DEseq() command, or should I keep it on? Will it skew results if I run the independent filter on already pre-filtered data? Please let me know.

[ATpoint]

Leave it on. Just follow the manual. It includes optional prefiltering and does not recommend to turn off IF. Don't reinvent the wheel. Follow the expert suggestions in the vignette.

Answer 1

[Michael Love]

Yes, repeating ATpoint, the default is to pre-filter and then use independent filtering.

Sometimes users want to have full p-values across a number of contrasts, so they choose to not use the independent filter, but just use a stronger pre-filter.