Showing : Contrast • reset
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
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5
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775
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
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4
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1.2k
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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
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3
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829
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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
18 months ago Edgar • 0
0
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1
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742
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
2
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3
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1.3k
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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
0
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1
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997
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago • updated 2.7 years ago slcno • 0
7
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9
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13k
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Contrasts in DESeq2
deseq2 contrast
updated 20 months ago by • 0 • written 3.5 years ago by ▴ 60
3
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2
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802
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LIMMA Time descendant design
limma time-dependant contrast
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 10
5
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10
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1.3k
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Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
1
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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
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2
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701
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same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 41k • written 4.5 years ago by • 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
4.5 years ago luciest.rodriguez • 0
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6
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1.2k
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 10 months ago by ▴ 10 • written 4.9 years ago by ▴ 90
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9
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2.0k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.2 years ago ariel ▴ 20
6
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7
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1.8k
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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
3
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5
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1.5k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
2
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1
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902
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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 5.4 years ago by 50k • written 5.4 years ago by • 0
1
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3
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3.6k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
5.5 years ago • updated 4.6 years ago Iryna • 0
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5
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1.4k
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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
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3
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1.0k
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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
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5
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2.4k
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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
5.9 years ago russell.stewart.j • 0
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4
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8.0k
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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 6.2 years ago by 50k • written 6.2 years ago by ▴ 20
9
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1
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4.4k
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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
2
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4
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1.5k
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Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 60
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2
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1.1k
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Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
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5
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2.3k
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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 6.6 years ago by 50k • written 6.7 years ago by ▴ 10
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2
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1.6k
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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
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 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
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4
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1.7k
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Time points and donors - errors with contrasts
deseq2 contrast
updated 6.4 years ago by 41k • written 6.8 years ago by • 0
2
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2
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2.1k
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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
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5
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5.2k
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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
0
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1
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1.4k
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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
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7
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3.6k
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Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
7.0 years ago Jeff Skinner • 0
3
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19
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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
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1
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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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13
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4.8k
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DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
7.2 years ago crfitzpat • 0
2
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3
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1.2k
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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
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2
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1.1k
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edgeR constrast drug treatments and time points
edgeR contrast
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
0
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3
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1.9k
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limma camera function Multiple contrasts
limma microarray contrast camera
updated 7.6 years ago by 50k • written 7.6 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 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 300
1
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6
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1.2k
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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
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2
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2.1k
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"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
2
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6
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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
2
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4
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5.4k
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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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5.5k
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DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago • updated 8.2 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 8.4 years ago by 41k • written 8.4 years ago by ▴ 60
4
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9
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2.1k
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How to construct contrasts for a linear model with interactions?
limma contrast linear model
8.4 years ago vedran.franke • 0
1
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4
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1.4k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
8.5 years ago arrigonialberto86 • 0
0
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1
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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
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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