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Showing :
contrasts
•
reset
3
votes
3
replies
1.2k
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
bioinf
▴ 10
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
JKim
• 0
0
votes
3
replies
1.7k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
a26fd14e
• 0
1
vote
2
replies
979
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
2.6 years ago
jovel_juan
▴ 30
3
votes
6
replies
1.9k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
3.1 years ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
1.2k
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
jeltje.van.baren
• 0
3
votes
8
replies
5.5k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 3.7 years ago by
Nicole
▴ 10
0
votes
3
replies
2.2k
views
limma voom contrasts
contrasts
limma
voom
updated 3.9 years ago by
Gordon Smyth
53k • written 3.9 years ago by
S T
▴ 90
0
votes
1
reply
1.1k
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
Mir
• 0
0
votes
2
replies
1.5k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
4.4 years ago
James
• 0
0
votes
3
replies
1.7k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
Mir
• 0
2
votes
8
replies
3.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
4.7 years ago • updated 4.6 years ago
Jane
▴ 10
3
votes
8
replies
2.0k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 6.1 years ago by
James W. MacDonald
68k • written 6.1 years ago by
s.connell
• 0
0
votes
1
reply
1.5k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
ananda2
• 0
0
votes
0
replies
1.1k
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
6.1 years ago
ingerslev
• 0
0
votes
1
reply
1.6k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
ananda2
• 0
2
votes
3
replies
2.0k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
Keith Hughitt
▴ 180
0
votes
4
replies
1.7k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 6.3 years ago by
Gordon Smyth
53k • written 6.3 years ago by
uridavid.akavia
• 0
0
votes
1
reply
1.0k
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
kehoe
• 0
3
votes
5
replies
2.1k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 6.8 years ago by
Aaron Lun
★ 29k • written 6.8 years ago by
Pietro
▴ 40
2
votes
6
replies
1.7k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 6.9 years ago by
Gordon Smyth
53k • written 6.9 years ago by
Maiv
• 0
21 results • Page
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Recent ...
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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