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Showing :
contrast
•
reset
3
votes
19
replies
3.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.1 years ago
mheydarpour
▴ 10
3
votes
16
replies
4.1k
views
limma contrast matrix
limma
contrast
design and contrast matrix
9.5 years ago • updated 9.4 years ago
Smith H.
▴ 20
2
votes
13
replies
4.8k
views
DESeq2 log fold change estimates for factors with many levels
deseq2
lfce
contrast
7.2 years ago
crfitzpat
• 0
5
votes
11
replies
11k
views
DESeq2: with multiple factors and interaction terms won't show all effects
deseq2
multiple factor design
contrast
interactions
updated 9.2 years ago by
Michael Love
41k • written 9.2 years ago by
mat.lesche
▴ 90
5
votes
10
replies
1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2
DGE
contrast
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
llooll1
• 0
0
votes
9
replies
2.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.2 years ago
ariel
▴ 20
7
votes
9
replies
13k
views
Contrasts in DESeq2
deseq2
contrast
updated 20 months ago by
梓琪
• 0 • written 3.6 years ago by
bahmanik@msu.edu
▴ 60
8
votes
9
replies
4.3k
views
DESeq2: Compare expression of one group to the mean of others
deseq2
heterosis
contrast
design and contrast matrix
updated 8.8 years ago by
Michael Love
41k • written 8.8 years ago by
johntlovell
▴ 10
4
votes
9
replies
2.1k
views
How to construct contrasts for a linear model with interactions?
limma
contrast
linear model
8.4 years ago
vedran.franke
• 0
2
votes
8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2
interactions
contrast
8.9 years ago
shao
▴ 100
17
votes
7
replies
13k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
Anke Busch
▴ 10
0
votes
7
replies
3.6k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger
contrast
covariate
glmlrt()
7.0 years ago
Jeff Skinner
• 0
6
votes
7
replies
1.8k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2
contrast
ratio of ratio
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
Fischer-philipp
▴ 30
2
votes
6
replies
1.8k
views
Seeking confirmation on manually setting contrasts for a 3-factor design in DESeq2 with multiple interaction terms
deseq2
multiple factor design
interactions
design and contrast matrix
contrast
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
piensaglobalmente
▴ 10
2
votes
6
replies
3.3k
views
voom/limma contrast for comparing one level against base-line
limma
voom
contrast
updated 9.1 years ago by
Steve Lianoglou
★ 13k • written 9.1 years ago by
Stijn van Dongen
▴ 80
1
vote
6
replies
1.2k
views
Are these contrasts correct for use in DESeq2?
deseq2
contrast
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
Jane Merlevede
▴ 90
2
votes
6
replies
1.4k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de
contrast
design and contrast matrix
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
nooshin
▴ 300
1
vote
6
replies
1.2k
views
dseq2 results synergy contrast
deseq2
contrast
synergy
updated 10 months ago by
Jane
▴ 10 • written 4.9 years ago by
steven wink
▴ 90
2
votes
5
replies
5.2k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2
results
contrast
padj
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
courtney.stairs
• 0
2
votes
5
replies
2.4k
views
Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?
limma
contrast
missing data
lmfit
makecontrasts
updated 6.6 years ago by
Gordon Smyth
50k • written 6.7 years ago by
wewolski
▴ 10
3
votes
5
replies
1.5k
views
pass limma contrast matrix variable
contrast
limma
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
John linux-user
▴ 210
0
votes
5
replies
775
views
Model and Contrasts with 4 variables
contrast
edgeR
DESeq2
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
Cristina
• 0
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2
lfcshrink
contrast
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
jurbach
▴ 10
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2
LRT
multifactor
contrast
interactions
8.3 years ago • updated 8.2 years ago
rclaire
▴ 20
0
votes
5
replies
1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2
rna-seq
interactions
contrast
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
Maithê Barros
▴ 10
1
vote
5
replies
2.4k
views
DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2
multiple factor design
contrast
5.9 years ago
russell.stewart.j
• 0
0
votes
4
replies
1.2k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
Michael
• 0
2
votes
4
replies
5.4k
views
Interaction terms in DESeq2 contrasts
deseq2
interactions
design and contrast matrix
contrast
8.1 years ago
dwzhang.wisc
▴ 20
0
votes
4
replies
1.7k
views
Time points and donors - errors with contrasts
deseq2
contrast
updated 6.4 years ago by
Michael Love
41k • written 6.8 years ago by
sasha
• 0
1
vote
4
replies
1.4k
views
Specificity of gene expression
differential gene expression
specific expression
contrast
deseq2
8.5 years ago
arrigonialberto86
• 0
2
votes
4
replies
1.5k
views
Multiple test corrections for planed contrasts
deseq2
multiple comparisons
contrast
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
serpalma.v
▴ 60
4
votes
4
replies
8.0k
views
edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger
design and contrast matrix
contrast
limma contrast matrix
limma
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
cafelumiere12
▴ 20
0
votes
4
replies
1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2
contrast
design
4.6 years ago • updated 4.5 years ago
luciest.rodriguez
• 0
2
votes
3
replies
1.2k
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2
contrast
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
sebastiano.curreli
• 0
2
votes
3
replies
1.3k
views
Contrast treated samples against both scramble and untreated controls
design
contrast
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
oliver.ziff
• 0
0
votes
3
replies
830
views
I have a problem when I run DESeq2 with one variable with 8 levels, I can't find the contrast for any comparison with level 8
Contrast
factors
levels
18 months ago
Edgar
• 0
0
votes
3
replies
3.4k
views
Where to include an interaction term in DESeq2
deseq2
contrast
design
updated 9.3 years ago by
Michael Love
41k • written 9.3 years ago by
ksilkaitis
• 0
0
votes
3
replies
1.0k
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2
contrast
results
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
jan.soderman
• 0
0
votes
3
replies
1.9k
views
limma camera function Multiple contrasts
limma
microarray
contrast
camera
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
gaby8638
▴ 20
1
vote
3
replies
3.6k
views
Multi-factor analysis Deseq2
deseq2
contrast
LTR
5.5 years ago • updated 4.6 years ago
Iryna
• 0
0
votes
2
replies
1.1k
views
Discrepancy in extracting contrasts
deseq2
resultsnames
batch effect
contrast
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
pkachroo
▴ 10
0
votes
2
replies
701
views
same results changing contrast function
deseq2
contrast
DEG
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
ire.ontiveros
• 0
6
votes
2
replies
4.8k
views
All same padj of contrast results in the DESeq2
deseq2
padj
contrast
results
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
jjinhyoungkim
▴ 20
3
votes
2
replies
803
views
LIMMA Time descendant design
limma
time-dependant
contrast
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
anoopta88
▴ 10
1
vote
2
replies
216
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
5 weeks ago • updated 29 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
1.1k
views
edgeR constrast drug treatments and time points
edgeR
contrast
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
sergio.martinezcuesta
▴ 10
0
votes
2
replies
1.6k
views
DESEq2 contrast statement syntax and design statement question
deseq2
interactions
contrast
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
grashow
▴ 10
2
votes
2
replies
2.1k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR
ANOVA
t-test
contrast
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
Maiv
• 0
2
votes
2
replies
2.1k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2
rnaseq
contrast
multiple comparisons
fdrtool
7.9 years ago
sebastiano.curreli
• 0
9
votes
1
reply
4.4k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
serpalma.v
▴ 60
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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