[BioC] how to use color to represent significant changed genes in maPlot of edgeR

[Wang Peter]

dear ALL:

I can plot the MA pic,but donot know how to use the color.
there is a parameter in the function maPlot
de.tags.
do i need assign each gene a -1,0 or 1 to represent sig
down-regulated, no change or up

such is the related coding:


et <- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise")
summary(de <- decideTestsDGE(et, p=0.05, adjust="BH"))
result <- topTags(et, n=dim(d)[1], adjust.method="BH", sort.by="p.value")
write.table(result,file = "t0h_c0h",sep = "\t")

maPlot(logAbundance=unlist(result$table["logCPM"]),
logFC=unlist(result$table["logFC"]))


-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
Cornell University
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