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1
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25k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 41k • written 4.3 years ago by ★ 1.5k
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 41k • written 6.7 years ago by ▴ 10
7
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9
replies
13k
views
Contrasts in DESeq2
deseq2 contrast
updated 20 months ago by • 0 • written 3.6 years ago by ▴ 60
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 41k • written 9.2 years ago by ▴ 90
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 50k • written 6.2 years ago by ▴ 20
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
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
2
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5
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5.2k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
6
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2
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4.8k
views
All same padj of contrast results in the DESeq2
deseq2 padj contrast results
updated 8.7 years ago by 41k • written 8.7 years ago by ▴ 20
2
votes
13
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4.8k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
7.2 years ago crfitzpat • 0
9
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1
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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 41k • written 6.3 years ago by ▴ 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 41k • written 8.8 years ago by ▴ 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
1
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3
replies
3.6k
views
Multi-factor analysis Deseq2
deseq2 contrast LTR
5.5 years ago • updated 4.6 years ago Iryna • 0
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
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
0
votes
3
replies
3.4k
views
Where to include an interaction term in DESeq2
deseq2 contrast design
updated 9.3 years ago by 41k • written 9.3 years ago by • 0
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 ★ 13k • written 9.1 years ago by ▴ 80
2
votes
8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.9 years ago shao ▴ 100
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.4 years ago by 41k • written 8.4 years ago by ▴ 60
1
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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
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 50k • written 6.7 years ago by ▴ 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 ★ 28k • written 6.8 years ago by • 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
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
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
0
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3
replies
1.9k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 7.6 years ago by 50k • written 7.6 years ago by ▴ 20
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 41k • written 8.0 years ago by ▴ 10
6
votes
7
replies
1.8k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 5.2 years ago by 41k • written 5.2 years ago by ▴ 30
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 luciest.rodriguez • 0
0
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4
replies
1.7k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 6.4 years ago by 41k • written 6.8 years ago by • 0
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 8.6 years ago by 41k • written 8.6 years ago by ▴ 20
0
votes
2
replies
1.6k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
0
votes
1
reply
1.6k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 7.1 years ago by 41k • written 7.1 years ago by • 0
2
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4
replies
1.5k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 60
3
votes
5
replies
1.5k
views
pass limma contrast matrix variable
contrast limma
updated 8.6 years ago by 50k • written 8.6 years ago by ▴ 210
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
0
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5
replies
1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 10
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 ★ 28k • written 7.9 years ago by ▴ 300
0
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1
reply
1.4k
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 7.0 years ago by 41k • written 7.0 years ago by ▴ 90
1
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4
replies
1.4k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
8.5 years ago arrigonialberto86 • 0
5
votes
10
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1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 3.9 years ago by 41k • written 3.9 years ago by • 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 41k • written 2.5 years ago by • 0
1
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6
replies
1.2k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 90
2
votes
3
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1.2k
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
0
votes
4
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1.2k
views
Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
1
vote
6
replies
1.2k
views
dseq2 results synergy contrast
deseq2 contrast synergy
updated 10 months ago by ▴ 10 • written 4.9 years ago by ▴ 90
0
votes
2
replies
1.1k
views
Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
0
votes
2
replies
1.1k
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
0
votes
3
replies
1.0k
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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