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Showing :
Contrasts
•
reset
3
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3
replies
741
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 10 months ago by
ATpoint
★ 4.7k • written 10 months ago by
bioinf
▴ 10
2
votes
3
replies
736
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 11 months ago by
Gordon Smyth
52k • written 11 months ago by
JKim
• 0
0
votes
3
replies
1.2k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
a26fd14e
• 0
1
vote
2
replies
781
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
20 months ago
jovel_juan
▴ 30
3
votes
6
replies
1.5k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
2.2 years ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
899
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 2.3 years ago by
Gordon Smyth
52k • written 2.3 years ago by
jeltje.van.baren
• 0
3
votes
8
replies
4.6k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 2.8 years ago by
Nicole
▴ 10
0
votes
3
replies
1.8k
views
limma voom contrasts
contrasts
limma
voom
updated 3.0 years ago by
Gordon Smyth
52k • written 3.0 years ago by
S T
▴ 90
0
votes
1
reply
944
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Mir
• 0
0
votes
2
replies
1.2k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
3.5 years ago
James
• 0
0
votes
3
replies
1.3k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.6 years ago by
Mir
• 0
2
votes
8
replies
2.6k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
3.8 years ago
Jane
▴ 10
3
votes
8
replies
1.6k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
s.connell
• 0
0
votes
1
reply
1.3k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
ananda2
• 0
0
votes
0
replies
873
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
5.2 years ago
ingerslev
• 0
0
votes
1
reply
1.4k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
ananda2
• 0
2
votes
3
replies
1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
Keith Hughitt
▴ 180
0
votes
4
replies
1.2k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 5.4 years ago by
Gordon Smyth
52k • written 5.4 years ago by
uridavid.akavia
• 0
0
votes
1
reply
857
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
kehoe
• 0
3
votes
5
replies
1.7k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Pietro
▴ 40
2
votes
6
replies
1.4k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
Maiv
• 0
21 results • Page
1 of 1
Recent ...
Replies
Comment: Error in retrieving clinical data
by
boidnoid
• 0
I was having the same problem. You can check the answer in a [previous post][1]. Specifically, reinstalling the devel version from GitHub …
Answer: How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differenti
by
James W. MacDonald
68k
The short answer is yes. When you compute pseudo-bulk estimates, the counts/gene are expected to be somewhat proportional to the number of …
Comment: displaying the differential expression with deseq2 over 4X2 samples with the in
by
Leonard
• 0
Visualize subject contributions to overall differential expression using: Volcano plots/scatter plots (subject-colored). Heatmaps (subject…
Comment: Plot title for PCA in DESeq2
by
AL
• 0
Thank you!
Answer: Interpreting DESEQ2 interaction term and inclusion of covariate
by
swbarnes2
★ 1.4k
"ecotypehigh.rearing_high" will basically do a 4 group comparison, and tell you if any genes that change going from high to low change diff…
Votes
Interpreting DESEQ2 interaction term and inclusion of covariate
A: Seurat/DESeq2 - single cell RNA-seq differential expression
Answer: Plot title for PCA in DESeq2
A: DESeq2: detect significantly increasing across an ordinal variable
Answer: DEseq2 design for additive treatment
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