Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
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fawazfebin ▴ 60
@fawazfebin-14053
Last seen 4.4 years ago

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.

edger differential gene expression upregulated genes downregulated genes • 1.9k views
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@gordon-smyth
Last seen 11 hours ago
WEHI, Melbourne, Australia

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, ]

 

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

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@ryan-c-thompson-5618
Last seen 6 weeks ago
Icahn School of Medicine at Mount Sinai…

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.

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