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

Wang Peter wng.peter at gmail.com
Tue Mar 19 04:36:27 CET 2013

dear ALL:

I can plot the MA pic,but donot know how to use the color.
there is a parameter in the function maPlot
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")


shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu

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