Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
glmlrt()
•
reset
2
votes
2
replies
1.3k
views
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()
7.0 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 • updated 7.3 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 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
carlgdeboer
• 0
5
votes
7
replies
3.7k
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
1 of 1
Recent ...
Replies
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Awards
• All
Popular Question
to
James W. MacDonald
65k
Scholar
to
Michael Love
41k
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Locations
• All
Switzerland,
6 minutes ago
Germany,
7 minutes ago
United Kingdom,
9 minutes ago
Germany,
15 minutes ago
United States,
25 minutes ago
Traffic: 1034 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6