User: David ROUX

gravatar for David ROUX
David ROUX10
Reputation:
10
Status:
New User
Location:
France (Avignon University)
Last seen:
3 months, 3 weeks ago
Joined:
2 years, 10 months ago
Email:
d*********@univ-avignon.fr

Posts by David ROUX

<prev • 12 results • page 1 of 2 • next >
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Answer: A: How to retreive topGO significant IDs of genes after enrichment test ?
... I am answering my own question (in case it will help someone later). :-) I found the solution from other topics elsewhere (https://support.bioconductor.org/p/65856/ and https://www.biostars.org/p/239032/ ). A simple way is to re-use the “genesOfInterest” list created earlier in the topGO pipeline ...
written 3 months ago by David ROUX10
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How to retreive topGO significant IDs of genes after enrichment test ?
... Hello, I ran a topGO enrichement on my RNAseq data, the output looks: > allRes GO.ID Term Annotated Significant Expected classicFisher 1 GO:0043531 ADP binding 406 21 4.05 6.5e-10 ...
topgo enrichment genes significant ids written 3 months ago by David ROUX10
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Comment: C: Small problem of legend color in PCA, is it a bug or a my script miswriting ?
... I agree, I am sorry for that. Accordingly I made a copy of my question on the Sta... Over... forum. Thanks. ...
written 5 months ago by David ROUX10
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(Closed) Small problem of legend color in PCA, is it a bug or a my script miswriting ?
... Hello, I am following the DESeq2 pipeline. My design has 2 genotypes and 2 treatments. I ran the PCA to make a nice exploration of my RNAseq data. Everything look well excepted the legend that appears all black for the 2 genotypes (see the Genotype legend on right of the picture) while the PCA itse ...
pca color legend geom written 5 months ago by David ROUX10
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Comment: C: DESeq2: two genotypes, one treatment
... Thanks for your rapid and kind help ! :-) ...
written 6 months ago by David ROUX10
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Comment: C: DESeq2: two genotypes, one treatment
... Thanks. I got : > resultsNames(dds) [1] "Intercept" "Genotype_B_vs_A" "GenotypeA.TreatmentTreated" "GenotypeB.TreatmentTreated" So, I suppose that : "GenotypeA.TreatmentTreated" will answer question 1; "GenotypeB.TreatmentTreated" will answer question 2; Can we interpret the "Genotype_B_vs ...
written 6 months ago by David ROUX10
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Comment: C: DESeq2: two genotypes, one treatment
... Both are interesting, I mean: 1/ Get the differentially expressed genes in genotype A in response to treatment 2/ Get the differentially expressed genes in genotype B in response to treatment 3/ Compare the transcriptome response of genotype A vs B (before and after treatment) A PCA would well refle ...
written 6 months ago by David ROUX10
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DESeq2: two genotypes, one treatment
... Hello, I am new to DESeq2. The vignette (LINK) focuses on a simple set : "treated vs untreated ". My experimental design contains 2 genotypes (A and B) vs 2 conditions (Control / Treated). My coldata : Sample Genotype Treatment 1 A control 2 A control ...
deseq2 written 6 months ago by David ROUX10 • updated 6 months ago by Michael Love23k
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Comment: C: Filtering of RNA-seq data in EdgeR
... Thanks for your answer. (Next time I will post new thread). Elsewhere on the Web I asked if the final logCPM in a DGE analysis table was a mean of the CPM of the samples compared together. One gave me the answer "no". I am reassured by your answer. I was going to make a filter on positive logCPM, ...
written 2.9 years ago by David ROUX10
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Comment: C: edger, trended or common dispersion
... Ok, thanks for your response. David. ...
written 2.9 years ago by David ROUX10

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