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Showing :
contrasts
•
reset
3
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5
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1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Pietro
▴ 40
3
votes
8
replies
1.2k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 4.3 years ago by
James W. MacDonald
65k • written 4.3 years ago by
s.connell
• 0
3
votes
8
replies
3.2k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 23 months ago by
Nicole
▴ 10
3
votes
6
replies
925
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
15 months ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
220
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
2
votes
6
replies
1.1k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
Maiv
• 0
2
votes
8
replies
2.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
2.9 years ago • updated 2.8 years ago
Jane
• 0
2
votes
3
replies
1.3k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
Keith Hughitt
▴ 180
1
vote
3
replies
634
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
jeltje.van.baren
• 0
1
vote
2
replies
509
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
9 months ago
jovel_juan
▴ 30
0
votes
3
replies
595
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
a26fd14e
• 0
0
votes
1
reply
656
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
kehoe
• 0
0
votes
4
replies
943
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
uridavid.akavia
• 0
0
votes
1
reply
1.1k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
ananda2
• 0
0
votes
0
replies
658
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.3 years ago
ingerslev
• 0
0
votes
1
reply
992
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
ananda2
• 0
0
votes
1
reply
697
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Mir
• 0
0
votes
2
replies
937
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.6 years ago
James
• 0
0
votes
3
replies
1.2k
views
limma voom contrasts
contrasts
limma
voom
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
S T
▴ 90
0
votes
3
replies
956
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.6 years ago by
Kevin Blighe
★ 3.9k • written 2.6 years ago by
Mir
• 0
20 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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