Showing : contrast • reset
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 months ago Chanderkant Chaudhary • 0
0
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5
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926
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 13 months ago by 66k • written 13 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 17 months ago by ▴ 780 • written 17 months ago by • 0
0
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3
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912
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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
21 months ago Edgar • 0
0
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1
reply
804
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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 2.8 years ago by 42k • written 2.8 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
3.0 years ago • updated 2.9 years ago slcno • 0
7
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9
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15k
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Contrasts in DESeq2
deseq2 contrast
updated 24 months ago by • 0 • written 3.8 years ago by ▴ 60
3
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2
replies
866
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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
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 4.1 years ago by 42k • written 4.1 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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773
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same results changing contrast function
deseq2 contrast DEG
updated 4.7 years ago by 42k • written 4.7 years ago by • 0
0
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4
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1.8k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.8 years ago luciest.rodriguez • 0
1
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3
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3.8k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
5.7 years ago • updated 4.9 years ago Iryna • 0
1
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6
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1.3k
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 13 months ago by ▴ 10 • written 5.2 years ago by ▴ 90
0
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9
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2.1k
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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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1.6k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 10
2
votes
1
reply
959
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 5.7 years ago by 51k • written 5.7 years ago by • 0
0
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5
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1.5k
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 6.1 years ago by 42k • written 6.1 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
6.1 years ago russell.stewart.j • 0
4
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4
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8.3k
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 6.5 years ago by 51k • written 6.5 years ago by ▴ 20
9
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1
reply
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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1.6k
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
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Time points and donors - errors with contrasts
deseq2 contrast
updated 6.7 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 6.8 years ago by 42k • written 6.8 years ago by ▴ 10
2
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5
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2.5k
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 6.9 years ago by 51k • written 6.9 years ago by ▴ 10
0
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2
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1.7k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.0 years ago by 42k • written 7.0 years ago by ▴ 10
17
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7
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14k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 7.0 years ago by 42k • written 7.0 years ago by ▴ 10
2
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2
replies
2.2k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
2
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5
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5.5k
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
reply
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()
7.3 years ago Jeff Skinner • 0
3
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19
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3.8k
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 7.4 years ago by 42k • written 7.4 years ago by • 0
2
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13
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5.2k
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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1.5k
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
replies
1.4k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 8.2 years ago by 42k • written 8.2 years ago by ▴ 90
2
votes
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
8.2 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 8.3 years ago by 42k • written 8.3 years ago by ▴ 10
2
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4
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5.6k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.3 years ago dwzhang.wisc ▴ 20
2
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5
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5.7k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.5 years ago rclaire ▴ 20
6
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1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.7 years ago by 42k • written 8.7 years ago by ▴ 60
4
votes
9
replies
2.2k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
8.7 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
8.8 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 8.8 years ago by 42k • written 8.8 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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