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glmLRT()
•
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2
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2
replies
1.3k
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EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger
design matrix
glmlrt()
glmQFTest()
paired design
5.5 years ago
oakhamwolf
• 0
4
votes
15
replies
1.8k
views
Adjusting for procedural effect and deciding on statistical test
EdgeR
glmlrt()
ql f-test
7.5 years ago • updated 6.8 years ago
elineverbon
▴ 20
0
votes
7
replies
3.6k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger
contrast
covariate
glmlrt()
7.1 years ago
Jeff Skinner
• 0
1
vote
6
replies
1.1k
views
design of edgeR GLM test
edger
differential gene expression
glmlrt()
7.4 years ago
simarsidhu25
• 0
4
votes
7
replies
2.8k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger
differential gene expression
glmlrt()
7.4 years ago
simarsidhu25
• 0
7
votes
5
replies
3.5k
views
edgeR effects of design on testing main effects and interactions
edger
glmfit
glmlrt()
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
cadeans
• 0
4
votes
8
replies
1.9k
views
EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger
glmlrt()
differential expression
design and contrast matrix
updated 8.9 years ago by
Gordon Smyth
50k • written 8.9 years ago by
carlgdeboer
• 0
5
votes
7
replies
3.8k
views
How to specify 'contrast' in glmLRT command when treatments in design matrix are named with numbers, not letters
edger
rnaseq
glmlrt()
updated 9.1 years ago by
James W. MacDonald
65k • written 9.1 years ago by
MBWatson
• 0
6
votes
7
replies
7.2k
views
EdgeR: glmLRT(), Multifactorial designs and correction for multiple testing
edgeR
glmLRT()
multiple factor design
multiple testing correction
updated 9.3 years ago by
Aaron Lun
★ 28k • written 9.3 years ago by
Ekarl2
▴ 80
9 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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