User: mark.ebbert

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Posts by mark.ebbert

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Applying replaceOutliers rather than throwing out genes when model includes continuous variable
... 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 ...
rnaseq deseq2 differential expression differential gene expression written 23 months ago by mark.ebbert • 0 • updated 23 months ago by Michael Love ♦ 26k
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Comment: C: getGeneLengthAndGCContent: "zero or more than one input sequence"
... My apologies. Seems version was the problem. Not sure why because I installed everything fresh just a few months ago. ...
written 23 months ago by mark.ebbert • 0
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Comment: C: getGeneLengthAndGCContent: "zero or more than one input sequence"
... @daviderisso, I updated the post to include the smallest subset (with code) I could get to fail. Will that work? ...
written 23 months ago by mark.ebbert • 0
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Comment: C: getGeneLengthAndGCContent: "zero or more than one input sequence"
... @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 23 months ago by mark.ebbert • 0
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getGeneLengthAndGCContent: "zero or more than one input sequence"
... 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 ...
normalization biomart edaseq hg38 org.db written 23 months ago by mark.ebbert • 0 • updated 23 months ago by davide risso • 830
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Comment: C: Normalize to additional variable (brain weight) in DESeq2
... 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 2.1 years ago by mark.ebbert • 0
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Normalize to additional variable (brain weight) in DESeq2
... 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 ...
normalization cqn deseq2 normalized counts written 2.1 years ago by mark.ebbert • 0 • updated 2.1 years ago by Michael Love ♦ 26k

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