Question

Separate listing of up-regulated and down-regulated genes in edgeR DGE results.

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fawazfebin ▴ 60

@fawazfebin-14053

Last seen 3.8 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 • 1.7k views

ADD COMMENT • link updated 6.1 years ago by lisacarlon25 • 0 • written 6.1 years ago by fawazfebin ▴ 60

score 3 · Answer 1 · 2018-04-12

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Gordon Smyth 50k

@gordon-smyth

Last seen 4 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, ]

ADD COMMENT • link 6.1 years ago Gordon Smyth 50k

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

ADD REPLY • link 6.1 years ago fawazfebin ▴ 60

score 1 · Answer 2 · 2018-04-12

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Ryan C. Thompson ★ 7.9k

@ryan-c-thompson-5618

Last seen 9 months ago

Scripps Research, La Jolla, CA

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 COMMENT • link 6.1 years ago Ryan C. Thompson ★ 7.9k