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glmLRT()
•
reset
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
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
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
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 9.2 years ago by
James W. MacDonald
66k • written 9.2 years ago by
MBWatson
• 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()
7.4 years ago
simarsidhu25
• 0
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
1.2k
views
design of edgeR GLM test
edger
differential gene expression
glmlrt()
7.4 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 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
cadeans
• 0
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
9 results • Page
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Comment: Slightly different count plots from R and spreadsheet
by
Michael Love
42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM
by
Vitor
• 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). …
Comment: ChAMP installation issue
by
James W. MacDonald
66k
If you have beta values, try the `DSS` package. An alternative is to compute the logit transform (to M-values), which are amenable to analy…
Answer: pathview error
by
James W. MacDonald
66k
The obvious would be to check that you have genes that map to that pathway. It's unusual to have so many NA values for your NCBI gene IDs, …
Comment: ChAMP installation issue
by
Tahirah
• 0
Thanks a lot. But unfortunately it didn't work. I guess I will have to wait until ChAMP becomes available for version 3.19 In the meantime …
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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