Deseq2
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Sudip • 0
@d5b2591c
Last seen 21 days ago
Denmark

I am doing a Transcriptomics study, where I have 120 samples. I want to know what criteria should I set to filter counts. Below is what I am using now. But I think it maybe I can set the threshold fo the counts to a higher number. Has anyone have any experience in dealing with such big datasets. ```{r} keep <- rowSums(counts(dds)) >= 5 dds <- dds[keep,]

DESeq2 rnaseqGene • 212 views
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Cross-posted on biostars: https://www.biostars.org/p/9596031/

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ATpoint ★ 4.2k
@atpoint-13662
Last seen 17 hours ago
Germany

Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

It covers prefiltering (and everything else).

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