Pre-Filtering and Independent Filtering DESeq2
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16 months ago
turcoa1 • 0

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.

DESeq2 RNA-Seq Differential-Gene-Expression • 1.4k views
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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.

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15 months ago
Michael Love ★ 2.6k

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.

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