Showing : Contrast • reset
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
3 months ago Chanderkant Chaudhary • 0
0
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5
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887
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 12 months ago by 66k • written 12 months ago by • 0
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4
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1.4k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 16 months ago by ▴ 780 • written 16 months ago by • 0
0
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3
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893
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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
20 months ago Edgar • 0
0
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1
reply
787
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
2
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3
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1.4k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
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1
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1.1k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.9 years ago slcno • 0
7
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9
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14k
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Contrasts in DESeq2
deseq2 contrast
updated 23 months ago by • 0 • written 3.7 years ago by ▴ 60
3
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2
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835
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LIMMA Time descendant design
limma time-dependant contrast
updated 3.8 years ago by 66k • written 3.8 years ago by ▴ 10
5
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10
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1.4k
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Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
1
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1
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26k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.5 years ago by 42k • written 4.5 years ago by ★ 1.5k
0
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2
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744
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same results changing contrast function
deseq2 contrast DEG
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
0
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4
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1.7k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.7 years ago luciest.rodriguez • 0
1
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3
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3.7k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
5.7 years ago • updated 4.8 years ago Iryna • 0
1
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6
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1.2k
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 12 months ago by ▴ 10 • written 5.1 years ago by ▴ 90
0
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9
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2.1k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.4 years ago ariel ▴ 20
6
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7
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1.9k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 30
3
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5
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1.5k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 10
2
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1
reply
935
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EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR design matrix contrast
updated 5.6 years ago by 51k • written 5.6 years ago by • 0
0
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5
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1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 10
0
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3
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1.1k
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A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
1
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5
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2.5k
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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
6.0 years ago russell.stewart.j • 0
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4
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8.2k
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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 6.4 years ago by 51k • written 6.4 years ago by ▴ 20
9
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1
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4.6k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 60
2
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4
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1.5k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 6.6 years ago by 66k • written 6.6 years ago by ▴ 60
0
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4
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1.7k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 6.6 years ago by 42k • written 7.0 years ago by • 0
0
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2
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1.2k
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Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 6.7 years ago by 42k • written 6.7 years ago by ▴ 10
2
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5
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2.4k
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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 6.8 years ago by 51k • written 6.9 years ago by ▴ 10
0
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2
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1.7k
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 10
17
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7
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13k
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DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 10
2
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2
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2.2k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 7.0 years ago by ★ 28k • written 7.0 years ago by • 0
2
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5
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5.4k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 7.1 years ago by 42k • written 7.1 years ago by • 0
0
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1
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1.4k
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 7.2 years ago by 42k • written 7.2 years ago by ▴ 90
0
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7
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3.7k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
7.2 years ago Jeff Skinner • 0
3
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19
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3.7k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
7.3 years ago mheydarpour ▴ 10
0
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1
reply
1.6k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 7.3 years ago by 42k • written 7.3 years ago by • 0
2
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13
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5.0k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
7.4 years ago crfitzpat • 0
2
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3
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1.3k
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 7.4 years ago by 42k • written 7.4 years ago by • 0
0
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2
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1.2k
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 10
0
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3
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2.0k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 7.8 years ago by 51k • written 7.8 years ago by ▴ 20
2
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6
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1.4k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 300
1
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6
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1.3k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 8.1 years ago by 42k • written 8.1 years ago by ▴ 90
2
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2
replies
2.2k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
8.1 years ago sebastiano.curreli • 0
2
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6
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1.9k
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 8.2 years ago by 42k • written 8.2 years ago by ▴ 10
2
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4
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5.5k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.2 years ago dwzhang.wisc ▴ 20
2
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5
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5.6k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.4 years ago rclaire ▴ 20
6
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1
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2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.6 years ago by 42k • written 8.6 years ago by ▴ 60
4
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9
replies
2.1k
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How to construct contrasts for a linear model with interactions?
limma contrast linear model
8.6 years ago vedran.franke • 0
1
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4
replies
1.4k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
8.7 years ago arrigonialberto86 • 0
0
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1
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1.7k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 8.7 years ago by 42k • written 8.7 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Most sensible approach to a `stage*condition` design in DESeq2 by swbarnes2 ★ 1.4k
Doing a stage_treatment grouping is not the same as doing stage * treatment. You can use stage * treatment to compare one subgroup to anot…
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Votes
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
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