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5
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DESeq2 multifactor experiment design
deseq2
LRT
multifactor
contrast
interactions
8.2 years ago
rclaire
▴ 20
0
votes
4
replies
1.6k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2
contrast
design
4.5 years ago
luciest.rodriguez
• 0
2
votes
13
replies
4.7k
views
DESeq2 log fold change estimates for factors with many levels
deseq2
lfce
contrast
7.1 years ago
crfitzpat
• 0
2
votes
4
replies
5.3k
views
Interaction terms in DESeq2 contrasts
deseq2
interactions
design and contrast matrix
contrast
8.0 years ago
dwzhang.wisc
▴ 20
3
votes
19
replies
3.5k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.0 years ago
mheydarpour
▴ 10
0
votes
7
replies
3.5k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger
contrast
covariate
glmlrt()
7.0 years ago
Jeff Skinner
• 0
2
votes
6
replies
3.3k
views
voom/limma contrast for comparing one level against base-line
limma
voom
contrast
updated 9.0 years ago by
Steve Lianoglou
★ 13k • written 9.0 years ago by
Stijn van Dongen
▴ 80
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
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
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 6.7 years ago by
sasha
• 0
1
vote
4
replies
1.3k
views
Specificity of gene expression
differential gene expression
specific expression
contrast
deseq2
8.5 years ago • updated 8.4 years ago
arrigonialberto86
• 0
3
votes
16
replies
4.0k
views
limma contrast matrix
limma
contrast
design and contrast matrix
9.4 years ago
Smith H.
▴ 20
6
votes
2
replies
4.7k
views
All same padj of contrast results in the DESeq2
deseq2
padj
contrast
results
updated 8.6 years ago by
Michael Love
41k • written 8.6 years ago by
jjinhyoungkim
▴ 20
4
votes
9
replies
2.0k
views
How to construct contrasts for a linear model with interactions?
limma
contrast
linear model
8.4 years ago
vedran.franke
• 0
0
votes
1
reply
1.4k
views
how to extract complex contrast with DESeq2
contrast
DESeq2
differential gene expression
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
aec
▴ 90
2
votes
5
replies
5.1k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2
results
contrast
padj
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
courtney.stairs
• 0
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
16
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
2
replies
1.6k
views
DESEq2 contrast statement syntax and design statement question
deseq2
interactions
contrast
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
grashow
▴ 10
2
votes
5
replies
2.3k
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 6.6 years ago by
wewolski
▴ 10
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
2
votes
4
replies
1.5k
views
Multiple test corrections for planed contrasts
deseq2
multiple comparisons
contrast
updated 6.3 years ago by
James W. MacDonald
65k • written 6.3 years ago by
serpalma.v
▴ 60
9
votes
1
reply
4.3k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 6.2 years ago by
Michael Love
41k • written 6.2 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
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
5.8 years ago
russell.stewart.j
• 0
0
votes
3
replies
1.0k
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2
contrast
results
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
jan.soderman
• 0
0
votes
5
replies
1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2
rna-seq
interactions
contrast
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
Maithê Barros
▴ 10
1
vote
3
replies
3.6k
views
Multi-factor analysis Deseq2
deseq2
contrast
LTR
5.4 years ago • updated 4.5 years ago
Iryna
• 0
2
votes
1
reply
878
views
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR
design matrix
contrast
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
sdalin
• 0
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2
lfcshrink
contrast
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
jurbach
▴ 10
6
votes
7
replies
1.8k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2
contrast
ratio of ratio
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Fischer-philipp
▴ 30
0
votes
9
replies
1.9k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.1 years ago
ariel
▴ 20
1
vote
6
replies
1.1k
views
dseq2 results synergy contrast
deseq2
contrast
synergy
updated 9 months ago by
Jane
• 0 • written 4.8 years ago by
steven wink
▴ 90
0
votes
2
replies
685
views
same results changing contrast function
deseq2
contrast
DEG
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
ire.ontiveros
• 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
Assa Yeroslaviz
★ 1.5k
5
votes
10
replies
1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2
DGE
contrast
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
llooll1
• 0
3
votes
2
replies
785
views
LIMMA Time descendant design
limma
time-dependant
contrast
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
anoopta88
▴ 10
7
votes
9
replies
12k
views
Contrasts in DESeq2
deseq2
contrast
updated 20 months ago by
梓琪
• 0 • written 3.5 years ago by
bahmanik@msu.edu
▴ 60
0
votes
1
reply
951
views
Interaction using a single factor model DESeq2
synergy
DESeq2
RNA-seq
contrast
2.7 years ago • updated 2.6 years ago
slcno
• 0
1
vote
2
replies
141
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
2
votes
3
replies
1.2k
views
Contrast treated samples against both scramble and untreated controls
design
contrast
DESeq2
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
oliver.ziff
• 0
0
votes
5
replies
736
views
Model and Contrasts with 4 variables
contrast
edgeR
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
Cristina
• 0
0
votes
4
replies
1.1k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 13 months ago by
Basti
▴ 750 • written 13 months ago by
Michael
• 0
0
votes
1
reply
713
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast
design
DESeq2
continuous
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
tiansy
• 0
0
votes
3
replies
3.4k
views
Where to include an interaction term in DESeq2
deseq2
contrast
design
updated 9.2 years ago by
Michael Love
41k • written 9.2 years ago by
ksilkaitis
• 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 9.1 years ago by
Michael Love
41k • written 9.1 years ago by
mat.lesche
▴ 90
2
votes
8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2
interactions
contrast
8.8 years ago
shao
▴ 100
3
votes
5
replies
1.5k
views
pass limma contrast matrix variable
contrast
limma
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
John linux-user
▴ 210
0
votes
1
reply
1.6k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2
design and contrast matrix
interactions
contrast
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
moldach
▴ 20
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2
multiple factor design
experimental design
contrast
updated 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
anton.kratz
▴ 60
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Comment: Doing comparison of RNA-seq data using EdgeR
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Michael Love
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Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
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Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
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It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
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The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
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