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Question: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
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gravatar for fawazfebin
7 days 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 6 days ago by lisacarlon250 • written 7 days ago by fawazfebin30
3
gravatar for Gordon Smyth
7 days ago by
Gordon Smyth33k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth33k 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 7 days ago • written 7 days ago by Gordon Smyth33k

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

ADD REPLYlink written 7 days ago by fawazfebin30
1
gravatar for Ryan C. Thompson
7 days ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson6.5k 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 7 days ago by Ryan C. Thompson6.5k
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