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contrast matrix
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0
votes
2
replies
3.0k
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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 6.8 years ago by
relathman
▴ 20
3
votes
6
replies
2.2k
views
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
5
votes
5
replies
1.3k
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
65k • written 5.6 years ago by
mikhael.manurung
▴ 270
1
vote
2
replies
1.3k
views
differentially expressed genes without contrasts
limma
toptable
makecontrasts
contrast matrix
updated 6.8 years ago by
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
hoe
• 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
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 4.0 years ago by
Gordon Smyth
50k • written 4.1 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
0
votes
1
reply
1.1k
views
Syntax of DESeq2 contrast argument for all pairwise comparisons
deseq2
contrast matrix
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
natalie.hull
• 0
9 results • Page
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Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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