updated 8.4 years ago by
Gordon Smyth
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written 8.4 years ago by
Sara
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Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
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> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish
by
Michael Love
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Let me see if I can add some code to tximeta to cover this case.
I've added an argument `skipRanges` in devel branch which should allow:
…
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
Jonathan
▴
10
Thank you; I was indeed using `DGEList` on the count matrix, but with the multiple edits of the post I forgot to include this step.
BTW, …
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
The other reason for doing this is because when you do `topTable(fit)`, you will automatically annotate the output data.
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
If you have versioned Ensembl Gene IDs, you can always use "GENEIDVERSION" for the `select` statement, or just strip off the version number…
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