How can I get a list of the DE genes from edgeR?
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Rodrigo • 0
@rodrigo-24834
Last seen 16 months ago

I am trying to analyze the DE genes from rna-seq data, but when I try to use the goana function I get the error message "No annotated genes found in universe". I believe this is because the genes are annotated with the gene IDs from Ensembl instead of the ones from RefSeq. Nevertheless, I can still perform GO analyses with Ensembl ID with a different program, but I need a list of the DE genes so I can select them to proceed with the GO analyses. How can I get a list of the up and down regulated genes from the edgeR?

Best regards, Rodrigo.

GOanalyses edgeR DEgeneslist • 556 views
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Yunshun Chen ▴ 770
@yunshun-chen-5451
Last seen 3 days ago
Australia

See ?topTags

If you are interested in all the up- and down-regulated DE genes at an FDR cut-off of 0.05, you can try

out <- topTags(object, n = Inf, p = 0.05)$table DE.up <- out[out$logFC>0, ]
DE.down <- out[out\$logFC<0, ]

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calvin99 ▴ 10
@calvin99
Last seen 15 months ago
China

you can use 'FDR' and 'logFC' columns in the output of the function topTags