Question: DESeq2 setting significant p-value
0
5 months ago by
Merlin 10
Vancouver
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)
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 • 99 views
modified 5 months ago by Michael Love25k • written 5 months ago by Merlin 10
2
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.