DGEList remove/exclude rows with entrezgene = 'NA'
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belmore • 0
@belmore-15096
Last seen 3.2 years ago

Hello:

I have created and annotated a DGEList from RNA-seq data.

I would like to try EGSEA, however the DGEList$genes$entrezgene column has ~900 'NA' values.

Is there a way to remove rows with entrezgene values of 'NA' from the DGEList?

Thank you

edger dgelist NA egsea • 807 views
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@gordon-smyth
Last seen just now
WEHI, Melbourne, Australia

You can subset a DGEList as if it was a matrix. For example:

i <- is.na(dge$genes$entrezgene)
dge <- dge[!i, ]

This removes all the rows for which the Entrez Gene ID is NA.

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