User: David Rengel

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David Rengel70
Reputation:
70
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Trusted
Location:
European Union
Last seen:
18 hours ago
Joined:
3 years, 10 months ago
Email:
d***********@toulouse.inra.fr

Posts by David Rengel

<prev • 35 results • page 1 of 4 • next >
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Answer: A: RNASeq interaction between factors with edgeR when cpms tend to zero
... Thanks Aaron and Gordon for your invaluable  answers. Things are so much clearer now, thanks a lot. Best, David ...
written 9 days ago by David Rengel70
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RNASeq interaction between factors with edgeR when cpms tend to zero
... Hi, I am using edgeR to analyze RNASeq data and I wonder about how the interactions between two factors is dealt with, especially when the normalized cpm values tend to 0 on one of the factors. I have the factors “time” (T0/T30) and “genotype” (A,B,C). In order to build my contrasts I created a du ...
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Comment: C: Removing batch effect on edgeR when interactons are looked at
... Thanks a lot Aaron, Best wishes, David ...
written 7 weeks ago by David Rengel70
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Comment: C: Removing batch effect on edgeR when interactons are looked at
... Hi Aaron, Thanks a lot for your helpful reply, I had not thought about this way out. Let me ask: do you think I am "losing" any power from the fact that I would use only R1-coefficients or this is not the case cause the contrasts are going to be made on the fitted values along al 4 replicates. Tha ...
written 7 weeks ago by David Rengel70
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Removing batch effect on edgeR when interactons are looked at
... Hi, I am running some RNASeq analysis with two experimental factors, namely time (two-level factor) and genotype (three-level factor). In cases like this, I like using edgeR cause, among other reasons, it makeContrasts feature is very handy. Thus, I would create a design factor combining all levels ...
rnaseq edger statistics model matrix written 7 weeks ago by David Rengel70 • updated 7 weeks ago by Steve Lianoglou12k
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Comment: C: Three way-interaction on voom (limma) data, including a factor with > 2 levels
... Thanks a lot.  Best, David ...
written 4 months ago by David Rengel70
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Comment: C: Three way-interaction on voom (limma) data, including a factor with > 2 levels
... Hi Aaron, Thanks for such a helpful answer. Actually, I had started with a linear approach because I cuold not see how to implement a triple interaction on edgeR. HOwever, provided that I may do so with makeContrasts; I'd rather stick to the original edgeR pipeline. What do ou think? Thanks again. ...
written 4 months ago by David Rengel70
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Answer: A: Three way-interaction on voom (limma) data, including a factor with > 2 levels
... This anwser was deleted and added as a comment above ...
written 4 months ago by David Rengel70
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Three way-interaction on voom (limma) data, including a factor with > 2 levels
... Hi, I am treating some RNASeq data whose experimental design includes three factors. I am interested, at first, in retrieving those genes showing the triple interaction, using voom + lmFit. I’ve read several posts on the matter, but none answered my question, so much so considering that one of my f ...
rnaseq limma anova voom written 4 months ago by David Rengel70
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Comment: C: How to deal with low-depth RNA-Seq within DESeq2 or edgeR
... Hi Ryan Thanks for your message and your detail on filtering on Avelogcpm. I’ll explore that. I’ve given a reply to Aaron’s comment here above. But I would like to add that the total genome has 37K annotated genes. However, annotation is far from optimal, and most probably, “real” genes should be f ...
written 9 months ago by David Rengel70

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Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni

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