Entering edit mode
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
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format
I have passed an input in DESeq2 where my data has sorted gene names by A-Z, now in results it is not showing the gene names in result. now I want to know if it DESeq2 is sorting the result or not on the basis of pvalue or anything, or i just can use my previous expression file's list and then manually take out the DEGs.
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.