Question: DESeq2 setting significant p-value
0
gravatar for Merlin
7 weeks ago by
Merlin 10
Italy
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)
resultsNames(dds)
resLFC <- lfcShrink(dds, coef=2, res=res, type="apeglm")
resFile <-na.omit(resLFC)
resFile <-resFile[order(resFile$padj),]
write.csv(as.data.frame(resFile),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 • 64 views
ADD COMMENTlink modified 7 weeks ago by Michael Love24k • written 7 weeks ago by Merlin 10
Answer: DESeq2 setting significant p-value
2
gravatar for Michael Love
7 weeks ago by
Michael Love24k
United States
Michael Love24k 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 7 weeks ago by Michael Love24k
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