Question: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
0
gravatar for fawazfebin
17 months ago by
fawazfebin30
fawazfebin30 wrote:

Hi ,

Can anyone help me to separately list top up-regulated and down-regulated genes from the list of differentially expressed genes. Is there any command for the same? Thanks in advance.

ADD COMMENTlink modified 17 months ago by lisacarlon250 • written 17 months ago by fawazfebin30
Answer: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
3
gravatar for Gordon Smyth
17 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

There's no need for a special function in edgeR because it's easy using ordinary R programming:

tab <- as.data.frame(topTags( ... ))
tab[ tab$logFC > 0, ]
tab[ tab$logFC < 0, ]

 

ADD COMMENTlink modified 17 months ago • written 17 months ago by Gordon Smyth38k

As simple as that :) .Great thanks, Sir.
 

ADD REPLYlink written 17 months ago by fawazfebin30
Answer: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
1
gravatar for Ryan C. Thompson
17 months ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.4k wrote:

As far as I know, there is no separate function for this. Simply split or filter your results based on the sign of the logFC column.

ADD COMMENTlink written 17 months ago by Ryan C. Thompson7.4k
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