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User: mark.ebbert
mark.ebbert • 0
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Posts by mark.ebbert
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3
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... Hi,
I'm using DESeq2 on a fairly large data set with continuous variables. I've looked through the vignette and various questions within the forum to see how best to handle outliers when using continuous variables in the model. The vignette states the following:
`Note that with continuous variable ...
written 14 months ago by
mark.ebbert • 0
• updated
14 months ago by
Michael Love ♦ 21k
0
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... My apologies. Seems version was the problem. Not sure why because I installed everything fresh just a few months ago.
...
written 14 months ago by
mark.ebbert • 0
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... @daviderisso, I updated the post to include the smallest subset (with code) I could get to fail. Will that work?
...
written 14 months ago by
mark.ebbert • 0
0
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... @daviderisso, I apologize for the slow response. I've been trying to generate a *small* reproducible example. So far, the smallest group I've been able to find is 5000 Ensemble gene IDs. Let me see if I can narrow it down more.
...
written 14 months ago by
mark.ebbert • 0
2
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... Hi,
I'm trying to use getGeneLengthAndGCContent to normalize some RNASeq data. My data was aligned to hg38 and I used featureCounts to aggregate by Ensembl gene ID (GRCh38 v. 87). I used the following call:
> hsa.len.gc <- getGeneLengthAndGCContent(id=rownames(counts.no.sex), org="hsa", mod ...
written 14 months ago by
mark.ebbert • 0
• updated
14 months ago by
davide risso • 810
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... Thanks Mike. Why not do the same for GC content and transcript length? Scratch that. GC content and transcript lengths are per gene, where brain weight is a single value across all genes.
...
written 16 months ago by
mark.ebbert • 0
4
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... Hi,
I'm working on a whole-tissue (brain) RNASeq study in mice where there is substantial neuronal death over time. We have multiple ages. I'd like to normalize to brain weight and would appreciate feedback to make sure I'm not doing anything that would violate DESeq2's internal modeling.
I perfor ...
written 16 months ago by
mark.ebbert • 0
• updated
16 months ago by
Michael Love ♦ 21k
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