Hello, I have made a couple of figures in DESeq, the first should plot genes with adjusted p-value <0.05 in red with >0.05 genes in grey, and was made with:
plotMA(res,
+ col = ifelse(res$padj>0.05, "gray69", "red3"),
+ linecol = "#ff000080",
+ xlab = "mean of normalized counts", ylab = expression(log[2]~fold~change),
+ log = "x", cex=0.45)
> dev.off()
The second should just plot genes that have a p-value >0.05 (i.e. all the red ones from the first figure):
resSig = res[res$padj <0.05, ]
> plotMA(resSig)
And yet there are red points in the first (padj<0.05) that are not present in the second! Can anybody explain this to me? I have attached the two figures.
And on a related note, is it better to use the p-value or adjusted p-value that DESeq gives you?
Many thanks
Alex
plotMA(res,
+ col = ifelse(res$padj>0.05, "gray69", "red3"),
+ linecol = "#ff000080",
+ xlab = "mean of normalized counts", ylab = expression(log[2]~fold~change),
+ log = "x", cex=0.45)
> dev.off()
The second should just plot genes that have a p-value >0.05 (i.e. all the red ones from the first figure):
resSig = res[res$padj <0.05, ]
> plotMA(resSig)
And yet there are red points in the first (padj<0.05) that are not present in the second! Can anybody explain this to me? I have attached the two figures.
And on a related note, is it better to use the p-value or adjusted p-value that DESeq gives you?
Many thanks
Alex
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