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.
1 answer
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.
Log in to answer this question.
-
DESeq2 Normalization and Pre-Filtering
written by turcoa1 •
-
Should I normalize the data before or after filtering to a particular cell type?
written by gt •
-
Filtering low variance genes for WGCNA
written by pennakiza
-
Differential analysis isoform level or gene level ?
written by agtbeeman •
-
ATAC-Seq: Filter bams for differential analysis or not
written by srhic •
-
DESeq2: How to interpret numbers for independent filtering?
written by nattzy94 •
-
edger and continuous variables
written by adR
-
How to perform GSEAPreranked analysis in a proper manner?
written by Deepak Tanwar
-
Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuffdiff
written by Sreeraj Thamban
-
Turn Off Blast Search On Reverse Complement Strand In Blastn
written by Zhaorong
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.