User: David Rengel

gravatar for David Rengel
David Rengel70
Reputation:
70
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Trusted
Location:
European Union
Last seen:
5 months, 1 week ago
Joined:
5 years, 10 months ago
Email:
d***********@ipbs.fr

Posts by David Rengel

<prev • 53 results • page 2 of 6 • next >
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Comment: C: Trying to simplify Interaction analysis with edger, and propably failing to do s
... Ryan and Aaron, Thanks for your very helpful remarks, as ever. I will have a look at geneas, of which I was unaware. I am not up to date on limma for RNA-Seq, even though I have used it in the past. Concerning the 3-way contrast, I will use it but also will look at doubles etc. When I deal with int ...
written 19 months ago by David Rengel70
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Comment: C: Trying to simplify Interaction analysis with edger, and propably failing to do s
... Indeed, sorry about that. I've corrected it. Thanks. ...
written 19 months ago by David Rengel70
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Trying to simplify Interaction analysis with edger, and propably failing to do so?
... Hi, I am running a 3-factor analysis on RNA-Seq data. Plants have been inoculated with either bacteria or a mock solution; different timepoints after inoculation have been harvested and, finally, at every timepoint, two different tissues have been harvested: the directly inoculated tissue (“IN” tis ...
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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 23 months 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 23 months 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 23 months 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 23 months 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 2.0 years 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 ...

Latest awards to David Rengel

Great Question 16 months ago, created a question with more than 5,000 views. For DESeq2: NA on padj column when doing bonferroni
Popular Question 16 months ago, created a question with more than 1,000 views. For DESEq2 log2FoldChange and lfcSE calculations
Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni
Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni
Popular Question 2.8 years ago, created a question with more than 1,000 views. For edgeR glmLRT and interaction effect: an example
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni

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