Question: DESeq2 setting significant p-value
gravatar for Merlin
5 months ago by
Merlin 10
Merlin 10 wrote:

Hello everyone, I have a question about the p-value that comes out from DESeq2.

Here is the command line that I use:

res <- results(dds, alpha = 0.05)
resLFC <- lfcShrink(dds, coef=2, res=res, type="apeglm")
resFile <-na.omit(resLFC)
resFile <-resFile[order(resFile$padj),]
write.csv(,file="~/RNAseq/salmon_folder/file.csv", quote=F)

The p-value and padj have lots of values greated then 0.05 and I’m not sure if I have to remove this values before plotting this data like when I do an heatmap for example.

Thank you

deseq2 • 99 views
ADD COMMENTlink modified 5 months ago by Michael Love25k • written 5 months ago by Merlin 10
Answer: DESeq2 setting significant p-value
gravatar for Michael Love
5 months ago by
Michael Love25k
United States
Michael Love25k wrote:

This is totally up to you, but in the workflow we simply plot the top genes by variance. Others will subset to the genes in the FDR set.

ADD COMMENTlink written 5 months ago by Michael Love25k
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