User: David Rengel

gravatar for David Rengel
David Rengel70
Reputation:
70
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Trusted
Location:
European Union
Last seen:
1 month, 2 weeks ago
Joined:
4 years, 7 months ago
Email:
d***********@toulouse.inra.fr

Posts by David Rengel

<prev • 45 results • page 1 of 5 • next >
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Comment: C: Circumventing statistical non-significance on a triple interaction using edgeR
... Thanks Aaron for your remarks, with which I completely agree. I understand the "depth" problem etc, i.e. the eventual lack of information at T0. However, it is also true that, in fact, many genes are not expressed at T0 and they are only expressed upon bacterial inoculation, whose effects are seen a ...
written 7 weeks ago by David Rengel70
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Circumventing statistical non-significance on a triple interaction using edgeR
... Hi, I have already discussed in the past this experimental design in which I deal with three factors (inoc: Bact or Mock; tissue: IN or OUT and hpi: 0,1,2,4 and 6h). Indeed, I am interested in the triple interaction, written on edgeR as:  ((Bact.IN.Tx - MOCK.IN.Tx) – (Bact.IN.T0 - MOCK.IN.T0)) – ...
rnaseq edger interactions makecontrasts written 7 weeks ago by David Rengel70 • updated 7 weeks ago by Aaron Lun20k
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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 4 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 4 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 8 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 8 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 8 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 8 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 ...

Latest awards to David Rengel

Popular Question 3 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 edgeR glmLRT and interaction effect: an example
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni

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