Showing : Contrast • reset
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227
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 4 days ago by ★ 5.0k • written 8 days ago by • 0
1
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2
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932
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
22 months ago Chanderkant Chaudhary • 0
0
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5
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1.4k
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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4
replies
2.8k
views
Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
0
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3
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1.3k
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
3.3 years ago Edgar • 0
0
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1
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1.2k
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
2
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3
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2.2k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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1
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1.6k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.5 years ago • updated 4.4 years ago slcno • 0
7
votes
9
replies
22k
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Contrasts in DESeq2
deseq2 contrast
updated 3.5 years ago by • 0 • written 5.3 years ago by ▴ 60
3
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2
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1.2k
views
LIMMA Time descendant design
limma time-dependant contrast
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
5
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10
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2.0k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
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1
reply
29k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ★ 1.5k
0
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2
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1.1k
views
same results changing contrast function
deseq2 contrast DEG
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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4
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2.5k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
6.3 years ago luciest.rodriguez • 0
1
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3
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4.5k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
7.2 years ago • updated 6.4 years ago Iryna • 0
1
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6
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1.8k
views
dseq2 results synergy contrast
deseq2 contrast synergy
updated 2.6 years ago by ▴ 10 • written 6.7 years ago by ▴ 90
0
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9
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3.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
6.9 years ago ariel ▴ 20
6
votes
7
replies
2.5k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 30
3
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5
replies
2.3k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
2
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1
reply
1.3k
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 7.2 years ago by 53k • written 7.2 years ago by • 0
0
votes
5
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1.9k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
0
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3
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1.5k
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A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
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5
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3.3k
views
DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2 multiple factor design contrast
7.6 years ago russell.stewart.j • 0
4
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4
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9.5k
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 8.0 years ago by 53k • written 8.0 years ago by ▴ 20
9
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1
reply
5.6k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
2
votes
4
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2.2k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 60
0
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4
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2.2k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 8.2 years ago by 43k • written 8.5 years ago by • 0
0
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2
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1.6k
views
Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 10
2
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5
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3.1k
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 8.4 years ago by 53k • written 8.4 years ago by ▴ 10
0
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2
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2.3k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
17
votes
7
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16k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 10
2
votes
2
replies
2.8k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
2
votes
5
replies
6.4k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
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1
reply
1.7k
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 90
0
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7
replies
4.4k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
8.8 years ago Jeff Skinner • 0
3
votes
19
replies
5.1k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.8 years ago mheydarpour ▴ 10
0
votes
1
reply
2.0k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
2
votes
13
replies
6.6k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
8.9 years ago crfitzpat • 0
2
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3
replies
1.8k
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
0
votes
2
replies
1.6k
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 9.2 years ago by ★ 29k • written 9.2 years ago by ▴ 10
0
votes
3
replies
2.5k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 20
2
votes
6
replies
2.0k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 300
1
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6
replies
1.8k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 90
2
votes
2
replies
2.8k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
9.7 years ago sebastiano.curreli • 0
2
votes
6
replies
2.5k
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 9.8 years ago by 43k • written 9.8 years ago by ▴ 10
2
votes
4
replies
6.7k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
9.8 years ago dwzhang.wisc ▴ 20
2
votes
5
replies
6.3k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
10.0 years ago rclaire ▴ 20
6
votes
1
reply
2.9k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 60
4
votes
9
replies
2.9k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
10.2 years ago vedran.franke • 0
1
vote
4
replies
1.8k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
10.3 years ago arrigonialberto86 • 0
59 results • Page 1 of 2
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This rotation style program sounds like a great way to explore different fields before committing to one. Similarly, apkgamex lets users ex…
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This compliance focused approach makes a lot of sense. Clear reminders and opt in policies help maintain trust, similar to how users look f…
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Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
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I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
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Answer: When to use edgeR or limma
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