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glmlrt()
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2
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1.2k
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EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger
design matrix
glmlrt()
glmQFTest()
paired design
5.1 years ago
oakhamwolf
• 0
4
votes
15
replies
1.6k
views
Adjusting for procedural effect and deciding on statistical test
EdgeR
glmlrt()
ql f-test
7.1 years ago • updated 6.4 years ago
elineverbon
▴ 20
0
votes
7
replies
3.4k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger
contrast
covariate
glmlrt()
6.6 years ago
Jeff Skinner
• 0
1
vote
6
replies
1.0k
views
design of edgeR GLM test
edger
differential gene expression
glmlrt()
7.0 years ago • updated 6.9 years ago
simarsidhu25
• 0
4
votes
7
replies
2.6k
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Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger
differential gene expression
glmlrt()
7.0 years ago
simarsidhu25
• 0
7
votes
5
replies
3.3k
views
edgeR effects of design on testing main effects and interactions
edger
glmfit
glmlrt()
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
cadeans
• 0
4
votes
8
replies
1.8k
views
EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger
glmlrt()
differential expression
design and contrast matrix
updated 8.4 years ago by
Gordon Smyth
48k • written 8.4 years ago by
carlgdeboer
• 0
5
votes
7
replies
3.4k
views
How to specify 'contrast' in glmLRT command when treatments in design matrix are named with numbers, not letters
edger
rnaseq
glmlrt()
updated 8.7 years ago by
James W. MacDonald
64k • written 8.7 years ago by
MBWatson
• 0
6
votes
7
replies
7.0k
views
EdgeR: glmLRT(), Multifactorial designs and correction for multiple testing
edgeR
glmLRT()
multiple factor design
multiple testing correction
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ekarl2
▴ 80
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Answer: EdgeR: Exact test and glmQLFTest produce very different results
by
James W. MacDonald
64k
You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.
Answer: limma::voom vs edgeR::voomLmFit - when to use?
by
James W. MacDonald
64k
The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…
Comment: 'Subtracting' counts on basis of Negative control media and water samples
by
Karthik
• 0
I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
by
James W. MacDonald
64k
It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor
by
arina
• 0
Hi Omer, Unfortunately I don't have an answer to your issue, but I am facing a very similar problem after integrating datasets that were …
Votes
A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Problem loading HDF5Array in R 4.3.2
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