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Contrasts
•
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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
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
0
votes
1
reply
655
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
941
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
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
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
1
reply
990
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
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
0
votes
1
reply
695
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
934
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.6 years ago
James
• 0
1
vote
2
replies
508
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
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
592
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
3
votes
5
replies
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
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
3
votes
6
replies
919
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
15 months ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
632
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
0
votes
3
replies
955
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
2
votes
3
replies
217
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
JKim
• 0
0
votes
0
replies
657
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.3 years ago
ingerslev
• 0
20 results • Page
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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…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
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
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
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