Question: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
0
gravatar for fawazfebin
11 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 11 months ago by lisacarlon250 • written 11 months ago by fawazfebin30
Answer: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
3
gravatar for Gordon Smyth
11 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k 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 11 months ago • written 11 months ago by Gordon Smyth36k

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

ADD REPLYlink written 11 months ago by fawazfebin30
Answer: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
1
gravatar for Ryan C. Thompson
11 months ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.2k 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 11 months ago by Ryan C. Thompson7.2k
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