User: David Rengel

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David Rengel70
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70
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Location:
European Union
Last seen:
2 months ago
Joined:
4 years, 1 month ago
Email:
d***********@toulouse.inra.fr

Posts by David Rengel

<prev • 40 results • page 1 of 4 • next >
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Comment: C: Loads, really loads of DEGs after edgeR differential analysis
... Hi Ryan and Aaron, Thank you both for your very helpful comments. I have run the analysis running glmTreat as suggested by Ryan, with logFC threshold =1. This dramatically decreases the number of DEGs, hence the firs point of Aaron's reply applies. I will have a look at a more robust parametrizatio ...
written 10 weeks ago by David Rengel70
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Comment: C: Loads, really loads of DEGs after edgeR differential analysis
... HI Ryan, Thanks a lot for your helpful reply. I had already tried using the new dispersion function but it gives me the following error: Error in .C("slocfit", x = as.numeric(x), y = as.numeric(rep(y, length.out = n)),  : "slocfit" not available for .C() for package "locfit" I guess this has to d ...
written 11 weeks ago by David Rengel70
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Comment: C: Loads, really loads of DEGs after edgeR differential analysis
... Yes, they are percentages. Please find below the real numbers and some code further below. Just note that what I call design factor corresponds to the modalities you may see on the contrasts and that reps, which I have implemented in the model, correspond to the replicate effect. Thanks again for yo ...
written 11 weeks ago by David Rengel70
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Comment: C: Loads, really loads of DEGs after edgeR differential analysis
... Hi Aaron, thanks for your quick reply. THe column correspond to the contrast I've looked at. They are simple comparisons between two conditions at a time: FOr instance GP vs G, GP vs Gpl etc. I attach here below the same table as above, but transposed, which looks better. For every condition there w ...
written 11 weeks ago by David Rengel70
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Loads, really loads of DEGs after edgeR differential analysis
... Hi, I am dealing with RNASeq data that render ludicrously hig number of DEGs in most of the contrasts I have tested. In the attached image file I reproduced the summary table of the analysis. The table shows percentages over the whole set, “NS” meaning non-significant (i.e. BH>0.05) and “UP” or ...
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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 3 months 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 4 months 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 4 months 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 4 months ago by David Rengel70 • updated 4 months ago by Steve Lianoglou12k

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Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni

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