Question: how to use color to represent significant changed genes in maPlot of edgeR
gravatar for wang peter
6.5 years ago by
wang peter2.0k
wang peter2.0k wrote:
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","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 Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at Facebook:
assign • 612 views
ADD COMMENTlink written 6.5 years ago by wang peter2.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 287 users visited in the last hour