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glmLRT()
•
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2
votes
2
replies
1.4k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger
design matrix
glmlrt()
glmQFTest()
paired design
5.6 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
7.6 years ago • updated 6.9 years ago
elineverbon
▴ 20
0
votes
7
replies
3.7k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger
contrast
covariate
glmlrt()
7.2 years ago
Jeff Skinner
• 0
1
vote
6
replies
1.2k
views
design of edgeR GLM test
edger
differential gene expression
glmlrt()
7.5 years ago
simarsidhu25
• 0
4
votes
7
replies
2.9k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger
differential gene expression
glmlrt()
7.5 years ago
simarsidhu25
• 0
7
votes
5
replies
3.6k
views
edgeR effects of design on testing main effects and interactions
edger
glmfit
glmlrt()
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 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 9.0 years ago by
Gordon Smyth
51k • written 9.0 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 9.3 years ago by
James W. MacDonald
66k • written 9.3 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 9.4 years ago by
Aaron Lun
★ 28k • written 9.4 years ago by
Ekarl2
▴ 80
9 results • Page
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Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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