User: Mauve

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Mauve0
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Norway
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2 years, 8 months ago
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2 years, 9 months ago
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Posts by Mauve

<prev • 6 results • page 1 of 1 • next >
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EdgeR:Calculating differential expression within/between groups in nested designs
... Hi, I have an RNA-seq experiment that is similar to section 3.5 in the edgeR user’s guide, i.e. a nested design, and I have used this approach to analyze my own data. Briefly, the experiment involves 60 RNA samples, corresponding to two groups of bacterial strains (commensal (C) and disease-causing ...
edger differential expression design matrix nested written 2.7 years ago by Mauve0 • updated 2.7 years ago by Aaron Lun17k
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Answer: A: RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
... Sorry for the late reply, and thank you Aaron for explaining how these design matrices can affect the dispersion estimates. I have now tried using both the one-way layout with four groups and a nested approach (model.matrix(~group+group:strain+group:condition)), but in either case I get the same BCV ...
written 2.8 years ago by Mauve0
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RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
... First, let me apologize in advance for posting a problem which might prove to be out of the scope of this forum. I am currently analysing data from a RNA-seq experiment in bacteria: The experiment involves 60 RNA samples, corresponding to two groups of bacterial strains (commensal (C) and disease- ...
edger rna-seq estimatedispersions bacteria written 2.8 years ago by Mauve0
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Answer: A: edgeR: estimating dispersion for nested designs
... Thank you for clarifying, I was under the impression that real biological replicates were required to estimate dispersion correctly, but I realize now that as I am only interested in group-level differences in expression between CTR and IND the strains can be considered as replicates. ...
written 2.8 years ago by Mauve0
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Comment: A: edgeR: estimating dispersion for nested designs
... So in the section 3.5 example, which option was used? ...
written 2.8 years ago by Mauve0
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edgeR: estimating dispersion for nested designs
... Hi, I have an RNA-seq experiment that is similar to section 3.5 in the edgeR user’s guide, i.e. a nested paired approach, and I have used this approach to analyze my own data. Briefly, the experiment involves 60 RNA samples, corresponding to two groups of bacterial strains (commensal (C) and diseas ...
edger estimatedispersions nested written 2.8 years ago by Mauve0

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend

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