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Contrasts
•
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3
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5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Pietro
▴ 40
3
votes
8
replies
1.2k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
s.connell
• 0
3
votes
8
replies
3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 24 months ago by
Nicole
▴ 10
3
votes
6
replies
978
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
279
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
JKim
• 0
2
votes
6
replies
1.1k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 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
Jane
▴ 10
2
votes
3
replies
1.4k
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
660
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
554
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
10 months ago
jovel_juan
▴ 30
0
votes
3
replies
646
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
a26fd14e
• 0
0
votes
1
reply
675
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
kehoe
• 0
0
votes
4
replies
977
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 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 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
ananda2
• 0
0
votes
0
replies
675
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.4 years ago
ingerslev
• 0
0
votes
1
reply
1.0k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
ananda2
• 0
0
votes
1
reply
717
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
960
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago
James
• 0
0
votes
3
replies
1.3k
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
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Mir
• 0
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James W. MacDonald
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So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
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Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano
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Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
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Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
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Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
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