I'm trying to get a mean expression plot, where only genes that are + - 0.6 LFC, and have a padj <0.001 to be in red. I have tried the following 2-3 things, but don't know how to get a plot where only the genes that are greater than 0.6 LFC and less than padj<0.001 to be in red. I''ve checked different forums and versions of DeSEQ2 vignettes.
## how to add a filter for LFC +- 0.6 to to this script: plot(log10(res$baseMean),res$log2FoldChange,xlab="mean expression",ylab="log fold change",pch=3,cex=0.5)
filt <- res$pvalue < 0.001
##or fix this script
plotMA(res, res$padj < 0.01 & res$log2FoldChangee > 0.5, main= "Differentially Expressed Genes", ylim=c(-1.5, 1.5))