Question

edgeR Differentially Expressed Genes

0

Entering edit mode

p_das • 0

@p_das-8653

Last seen 7.0 years ago

United States

Hi I am using edgeR for differential gene expression analysis. The following command : > summary(de <- decideTestsDGE(lrt.CHvsH)) gives me this result, > summary(de <- decideTestsDGE(lrt.CHvsH)) [,1] -1 1870 0 9649 1 515 How can the list of genes which are down regulated (1870 genes in this case), up regulated (515) and those which show no change (9649). Thank you Prerna

edger • 1.1k views

ADD COMMENT • link updated 8.6 years ago by Aaron Lun ★ 28k • written 8.6 years ago by p_das • 0

score 3 · Answer 1 · 2015-09-04

3

Entering edit mode

Aaron Lun ★ 28k

@alun

Last seen 3 hours ago

The city by the bay

Try this:

res <- topTags(lrt.CHvH, n=Inf, sort.by="none")$table
res[de==-1L,] # downregulated
res[de==1L,] # upregulated
res[de==0L,] # no change

ADD COMMENT • link 8.6 years ago Aaron Lun ★ 28k

0

Entering edit mode

Thanks a bunch Aaron!!

ADD REPLY • link 8.6 years ago p_das • 0

0

Entering edit mode

Aaron, you are the best...Thank you for helping me always..

ADD REPLY • link 8.6 years ago p_das • 0