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contrast matrix
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3
votes
6
replies
2.2k
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Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix
toptable
makecontrasts
differential gene expression
6.6 years ago
stinehedensted
• 0
4
votes
3
replies
1.3k
views
What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger
limma
model.matrix
contrast matrix
design matrix
updated 7.8 years ago by
Gavin Kelly
▴ 680 • written 7.8 years ago by
Peter
• 0
0
votes
1
reply
1.1k
views
Syntax of DESeq2 contrast argument for all pairwise comparisons
deseq2
contrast matrix
updated 7.3 years ago by
Michael Love
42k • written 7.3 years ago by
natalie.hull
• 0
0
votes
2
replies
3.0k
views
Time-course analysis with limma for >3 time points
limma
contrast matrix
design matrix
multiple time points
timecourse
updated 3.0 years ago by
rf
• 0 • written 6.9 years ago by
relathman
▴ 20
1
vote
2
replies
1.3k
views
differentially expressed genes without contrasts
limma
toptable
makecontrasts
contrast matrix
updated 6.9 years ago by
Ryan C. Thompson
★ 7.9k • written 6.9 years ago by
hoe
• 0
5
votes
5
replies
1.4k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma
design and contrast matrix
design matrix
contrast matrix
updated 5.6 years ago by
James W. MacDonald
66k • written 5.6 years ago by
mikhael.manurung
▴ 270
0
votes
4
replies
1.3k
views
Agilent two-color microarray analysis with limma: 2x3 factorial design
limma
microarray
contrast matrix
2x3 factorial design
differential expression
updated 4.1 years ago by
Gordon Smyth
50k • written 4.2 years ago by
Natalia
• 0
0
votes
8
replies
1.2k
views
Designating contrasts in diffSpliceDGE to test for nested effects
diffSpliceDGE
Contrast matrix
edger
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
rachel.steward
• 0
4
votes
7
replies
1.1k
views
Design matrix and contrast for RNA knockdown experiment
design matrix
limma
contrast matrix
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
maltethodberg
▴ 180
9 results • Page
1 of 1
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Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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