Showing : Contrast • reset
1
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
8 months ago • updated 7 months ago Chanderkant Chaudhary • 0
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5
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1.1k
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 17 months ago by 67k • written 17 months ago by • 0
0
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4
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1.8k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
0
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3
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1.0k
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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
2.1 years ago Edgar • 0
0
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1
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917
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
2
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3
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1.6k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
0
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1
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1.2k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.3 years ago slcno • 0
7
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9
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17k
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Contrasts in DESeq2
deseq2 contrast
updated 2.3 years ago by • 0 • written 4.1 years ago by ▴ 60
3
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2
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947
views
LIMMA Time descendant design
limma time-dependant contrast
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 10
5
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10
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1.5k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
1
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1
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27k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by ★ 1.5k
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2
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850
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same results changing contrast function
deseq2 contrast DEG
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
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4
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2.0k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
5.1 years ago luciest.rodriguez • 0
1
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3
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3.9k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
6.1 years ago • updated 5.2 years ago Iryna • 0
1
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6
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1.4k
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 17 months ago by ▴ 10 • written 5.5 years ago by ▴ 90
0
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9
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2.3k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.8 years ago ariel ▴ 20
6
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7
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2.0k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 30
3
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5
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1.7k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 10
2
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1
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1.0k
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 6.0 years ago by 51k • written 6.0 years ago by • 0
0
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5
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1.6k
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 6.2 years ago by 42k • written 6.2 years ago by ▴ 10
0
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3
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1.2k
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A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
1
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5
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2.7k
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DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2 multiple factor design contrast
6.4 years ago russell.stewart.j • 0
4
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4
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8.6k
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 6.8 years ago by 51k • written 6.8 years ago by ▴ 20
9
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1
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4.9k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 60
2
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4
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1.7k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 6.9 years ago by 67k • written 6.9 years ago by ▴ 60
0
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4
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1.8k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 7.0 years ago by 42k • written 7.4 years ago by • 0
0
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2
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1.3k
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Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 7.1 years ago by 42k • written 7.1 years ago by ▴ 10
2
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5
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2.6k
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 7.2 years ago by 51k • written 7.3 years ago by ▴ 10
0
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2
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1.8k
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.3 years ago by 42k • written 7.3 years ago by ▴ 10
17
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7
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14k
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DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 7.3 years ago by 42k • written 7.3 years ago by ▴ 10
2
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2
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2.4k
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EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
2
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5
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5.7k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 7.4 years ago by 42k • written 7.4 years ago by • 0
0
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1
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1.5k
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 7.5 years ago by 42k • written 7.5 years ago by ▴ 90
0
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7
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3.9k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
7.6 years ago Jeff Skinner • 0
3
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19
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4.1k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
7.7 years ago mheydarpour ▴ 10
0
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1
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1.7k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 7.7 years ago by 42k • written 7.7 years ago by • 0
2
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13
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5.6k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
7.8 years ago crfitzpat • 0
2
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3
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1.5k
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 7.8 years ago by 42k • written 7.8 years ago by • 0
0
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2
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1.3k
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
0
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3
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2.1k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 8.1 years ago by 51k • written 8.1 years ago by ▴ 20
2
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6
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1.6k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 300
1
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6
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1.5k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 8.5 years ago by 42k • written 8.5 years ago by ▴ 90
2
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2
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2.3k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
8.5 years ago sebastiano.curreli • 0
2
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6
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2.0k
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 8.6 years ago by 42k • written 8.6 years ago by ▴ 10
2
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4
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5.9k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.6 years ago dwzhang.wisc ▴ 20
2
votes
5
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5.8k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.8 years ago rclaire ▴ 20
6
votes
1
reply
2.6k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 9.0 years ago by 42k • written 9.0 years ago by ▴ 60
4
votes
9
replies
2.3k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
9.0 years ago vedran.franke • 0
1
vote
4
replies
1.5k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
9.1 years ago arrigonialberto86 • 0
0
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1
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1.8k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 9.1 years ago by 42k • written 9.1 years ago by ▴ 20
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Answer: Downloading Metagenomic Data with Higher Taxonomic Units by Levi Waldron ★ 1.1k
I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette…
Comment: Differene between the Wald and LRT test for time-series gene expression data by Denise • 0
This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units by elozanoe • 0
Hi! I'm facing the same problem. Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
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A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Answer: Differene between the Wald and LRT test for time-series gene expression data
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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