Showing : Contrast • reset
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
17 months ago Chanderkant Chaudhary • 0
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1.3k
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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4
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2.5k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by • 0
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3
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1.2k
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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
2.9 years ago Edgar • 0
0
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1
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1.1k
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
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3
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1.9k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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1
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1.4k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.1 years ago • updated 4.0 years ago slcno • 0
7
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9
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21k
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Contrasts in DESeq2
deseq2 contrast
updated 3.1 years ago by • 0 • written 4.9 years ago by ▴ 60
3
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2
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1.1k
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LIMMA Time descendant design
limma time-dependant contrast
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
5
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10
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1.9k
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Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
1
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1
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28k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ★ 1.5k
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2
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1.0k
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same results changing contrast function
deseq2 contrast DEG
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
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4
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2.4k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
5.9 years ago luciest.rodriguez • 0
1
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3
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4.3k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
6.8 years ago • updated 6.0 years ago Iryna • 0
1
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6
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1.7k
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 2.2 years ago by ▴ 10 • written 6.3 years ago by ▴ 90
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9
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2.7k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
6.5 years ago ariel ▴ 20
6
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7
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2.3k
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DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
3
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5
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2.0k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
2
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1
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1.2k
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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 6.8 years ago by 52k • written 6.8 years ago by • 0
0
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5
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1.8k
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
0
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3
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1.4k
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A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
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5
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3.1k
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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
7.2 years ago russell.stewart.j • 0
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4
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9.2k
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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 7.6 years ago by 52k • written 7.6 years ago by ▴ 20
9
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1
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5.4k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 60
2
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4
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1.9k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 60
0
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4
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2.1k
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Time points and donors - errors with contrasts
deseq2 contrast
updated 7.8 years ago by 43k • written 8.1 years ago by • 0
0
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2
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1.5k
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Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
2
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5
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2.9k
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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 8.0 years ago by 52k • written 8.0 years ago by ▴ 10
0
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2
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2.1k
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
17
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7
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15k
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DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
2
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2
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2.7k
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EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
2
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5
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6.2k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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1
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1.6k
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how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 90
0
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7
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4.2k
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Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
8.4 years ago Jeff Skinner • 0
3
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19
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4.7k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.4 years ago mheydarpour ▴ 10
0
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1
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1.9k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
2
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13
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6.3k
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DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
8.5 years ago crfitzpat • 0
2
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3
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1.7k
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Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 8.5 years ago by 43k • written 8.6 years ago by • 0
0
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2
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1.5k
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edgeR constrast drug treatments and time points
edgeR contrast
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 10
0
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3
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2.4k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 8.9 years ago by 52k • written 8.9 years ago by ▴ 20
2
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6
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1.8k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 9.2 years ago by ★ 29k • written 9.2 years ago by ▴ 300
1
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6
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1.7k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 9.3 years ago by 43k • written 9.3 years ago by ▴ 90
2
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2
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2.6k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
9.3 years ago sebastiano.curreli • 0
2
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6
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2.3k
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 9.4 years ago by 43k • written 9.4 years ago by ▴ 10
2
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4
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6.5k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
9.4 years ago dwzhang.wisc ▴ 20
2
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5
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6.1k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
9.6 years ago rclaire ▴ 20
6
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1
reply
2.8k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 60
4
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9
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2.7k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
9.8 years ago vedran.franke • 0
1
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4
replies
1.7k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
9.9 years ago arrigonialberto86 • 0
0
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1
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2.0k
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DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 20
58 results • Page 1 of 2
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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