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User: Matarit

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Matarit10
Reputation:
10
Status:
New User
Location:
France
Last seen:
2 years, 11 months ago
Joined:
3 years, 3 months ago
Email:
a*********@ifremer.fr

Posts by Matarit

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Big differences in logfoldchange for some genes between edgeR and DESeq2
... Thank you all for your help. I am re-running my analyses with and without shrinkage, and will compare my results. ...
written 3.2 years ago by Matarit10
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Comment: C: Big differences in logfoldchange for some genes between edgeR and DESeq2
... Thanks, that's very clear and makes sense for those genes. Would that be also true for genes almost not expressed in one condition and much more expressed in the other, or is it only true if you have low counts throughout all samples? ...
written 3.2 years ago by Matarit10
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Comment: C: Big differences in logfoldchange for some genes between edgeR and DESeq2
... Thanks again Michael and Aaron for your replies. I also indeed improperly asked my question: which logFC is the best estimator? Knowing that the sample size is set for my experiment. From you answers, I get that I cannot really answer that question.  But for the biology behind the experiment, how f ...
written 3.2 years ago by Matarit10
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Comment: C: Big differences in logfoldchange for some genes between edgeR and DESeq2
... Thank you Michael for your answer. I went through your article again. I had also read the user guide for both packages. I had plot the plotMA for both shrunken and unshrunken results in DESEq2, and the effect is very obvious. I understand each package makes different choices, but I am surprised by t ...
written 3.2 years ago by Matarit10
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Big differences in logfoldchange for some genes between edgeR and DESeq2
... Hi, I am currently analyzing a rna-seq dataset for differentially expressed genes between 2 conditions (20 individuals in condition A and 6 in B, B being the reference). I ran both DESeq2 and edgeR (glmFit and glmLRT) to compare my results with both methods. I have 51 DE genes with DESeq2, 156 with ...
edger deseq2 written 3.2 years ago by Matarit10 • updated 3.2 years ago by Gordon Smyth36k
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Comment: C: Problem with biomart's listMarts function
... Thanks! It works. I would not have thought about that as www was not an issue for ensembl.org. ...
written 3.3 years ago by Matarit10
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Comment: C: Problem with biomart's listMarts function
... Hi, I cannot get it work for www.metazoa.ensembl.org. I know the data set I need is there, any idea on how I can access it? Thank you for your help, list2=listMarts(host="www.metazoa.ensembl.org") Entity 'hellip' not defined Entity 'hellip' not defined Entity 'nbsp' not defined Entity 'raquo ...
written 3.3 years ago by Matarit10

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Big differences in logfoldchange for some genes between edgeR and DESeq2

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