Showing : Contrast • reset
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
9 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 18 months ago by 67k • written 18 months ago by • 0
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4
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1.9k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
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3
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1.1k
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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
2.2 years ago Edgar • 0
0
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1
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948
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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 43k • written 3.1 years ago by • 0
2
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3
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1.6k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 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
3.4 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 2.4 years ago by • 0 • written 4.2 years ago by ▴ 60
3
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2
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960
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LIMMA Time descendant design
limma time-dependant contrast
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 10
5
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10
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1.6k
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Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 4.5 years ago by 43k • written 4.5 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 4.9 years ago by 43k • written 4.9 years ago by ★ 1.5k
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2
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862
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same results changing contrast function
deseq2 contrast DEG
updated 5.1 years ago by 43k • written 5.1 years ago by • 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
5.2 years ago luciest.rodriguez • 0
1
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3
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4.0k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
6.2 years ago • updated 5.3 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 18 months ago by ▴ 10 • written 5.6 years ago by ▴ 90
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9
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2.4k
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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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2.1k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 5.9 years ago by 43k • written 5.9 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 43k • written 6.0 years ago by ▴ 10
2
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1
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1.1k
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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 6.1 years ago by 52k • written 6.1 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 6.3 years ago by 43k • written 6.3 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 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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5
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2.8k
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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
6.5 years ago russell.stewart.j • 0
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4
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8.6k
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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 6.9 years ago by 52k • written 6.9 years ago by ▴ 20
9
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1
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5.0k
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 43k • written 7.0 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 7.0 years ago by 67k • written 7.0 years ago by ▴ 60
0
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4
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1.9k
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Time points and donors - errors with contrasts
deseq2 contrast
updated 7.1 years ago by 43k • written 7.5 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 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
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5
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2.7k
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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 7.3 years ago by 52k • written 7.3 years ago by ▴ 10
0
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2
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1.9k
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.4 years ago by 43k • written 7.4 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 7.4 years ago by 43k • written 7.4 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 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
2
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5
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5.8k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
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1
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1.5k
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how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 90
0
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7
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3.9k
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Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
7.7 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 7.8 years ago by 43k • written 7.8 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
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Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
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2
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1.3k
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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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2.2k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 8.2 years ago by 52k • written 8.2 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 8.6 years ago by 43k • written 8.6 years ago by ▴ 90
2
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2
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2.4k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
8.6 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 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
2
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4
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5.9k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.7 years ago dwzhang.wisc ▴ 20
2
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5
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5.9k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.9 years ago rclaire ▴ 20
6
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1
reply
2.7k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 60
4
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9
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2.4k
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How to construct contrasts for a linear model with interactions?
limma contrast linear model
9.1 years ago vedran.franke • 0
1
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4
replies
1.5k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
9.2 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 9.2 years ago by 43k • written 9.2 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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