User: David Rengel

gravatar for David Rengel
David Rengel70
Reputation:
70
Status:
Trusted
Location:
European Union
Last seen:
5 months, 4 weeks ago
Joined:
5 years, 11 months ago
Email:
d***********@ipbs.fr

Posts by David Rengel

<prev • 53 results • page 1 of 6 • next >
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... Thanks a lot Gordon, it is clearer now. Best, David ...
written 5 months ago by David Rengel70
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... Hi James, Thanks, but is not it what I have done? I mean, there is a link to the figure. I've put a new imgur link just in case the previous one was not public. Hope it works. Best, David ...
written 6 months ago by David Rengel70
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... Hi, I am treating NovaSeq-produced RNA-Seq data with edgeR. In the analysis I look at what I call “strain” effect. There are DEGs for this factor that I find are biologically hard to explain. In the attached file, there are two examples. It is easy to see why they are declared as differentially expr ...
normalization edger differential expression rna-seq fitted values written 6 months ago by David Rengel70 • updated 6 months ago by Gordon Smyth39k
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Comment: C: limma random effects and multi level experiments
... Thanks a lot James. That was very helpful. Including the gl function, of which I was unaware! Best. David ...
written 7 months ago by David Rengel70
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Comment: C: limma random effects and multi level experiments
... ...Continued from previous comment (above) In others termes: it seems that by doing donor + treat, there are too many parameters to be estimated and one of them is left out. I hav obviously found myself in this scenario before but I do not recall it in a situation where I need to build contrasts wi ...
written 7 months ago by David Rengel70
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Comment: C: limma random effects and multi level experiments
... Hi Gordon, Thanks again for your suggestion. I have tried to implement it but I came across with this issue: the "reference" level of my treatment disappears under “donor + treatment” design. It obviously stays if I implement a “treatment + donor” design. I mean "reference" level because I do not wa ...
written 7 months ago by David Rengel70
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Answer: A: limma random effects and multi level experiments
... Thanks Mikhael, Aaron and Gordon for your kind replies. I apoligize for my late own reply. I will proceed as Gordon suggests. Best, David. ...
written 7 months ago by David Rengel70
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limma random effects and multi level experiments
... Hi, I have a question regarding limma-driven microarray analysis. I have a total of 24 arrays. My experimental design consists in two fixed factors, i.e. "matrix" (F or G) and "dim" (2 or 3), and what I consider a Random Factor, i.e. "donor". There are six donors, so that each donor has provided ...
limma multi-level random effect written 7 months ago by David Rengel70
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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 17 months 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 17 months ago by David Rengel70 • updated 17 months ago by Aaron Lun25k

Latest awards to David Rengel

Great Question 17 months ago, created a question with more than 5,000 views. For DESeq2: NA on padj column when doing bonferroni
Popular Question 17 months ago, created a question with more than 1,000 views. For DESEq2 log2FoldChange and lfcSE calculations
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni
Popular Question 19 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 3.7 years ago, created a question with more than 1,000 views. For DESeq2: NA on padj column when doing bonferroni

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