Showing : Contrast • reset
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
10 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 20 months ago by 67k • written 20 months ago by • 0
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4
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2.0k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 23 months ago by ▴ 780 • written 23 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
2.3 years ago Edgar • 0
0
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1
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981
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
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3
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1.7k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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1
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1.3k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.5 years ago slcno • 0
7
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9
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18k
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Contrasts in DESeq2
deseq2 contrast
updated 2.5 years ago by • 0 • written 4.3 years ago by ▴ 60
3
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2
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996
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LIMMA Time descendant design
limma time-dependant contrast
updated 4.3 years ago by 67k • written 4.3 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 4.6 years ago by 43k • written 4.6 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 5.0 years ago by 43k • written 5.0 years ago by ★ 1.5k
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2
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889
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same results changing contrast function
deseq2 contrast DEG
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
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4
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2.1k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
5.3 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
6.3 years ago • updated 5.4 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 19 months ago by ▴ 10 • written 5.7 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
6.0 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 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
3
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5
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1.8k
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lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 6.2 years ago by 43k • written 6.2 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 6.2 years ago by 52k • written 6.2 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 6.4 years ago by 43k • written 6.4 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 6.6 years ago by 43k • written 6.6 years ago by • 0
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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
6.6 years ago russell.stewart.j • 0
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4
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8.7k
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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 7.0 years ago by 52k • written 7.0 years ago by ▴ 20
9
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1
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5.1k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
2
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4
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1.8k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 7.2 years ago by 67k • written 7.2 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 7.2 years ago by 43k • written 7.6 years ago by • 0
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2
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1.4k
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Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
2
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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 7.4 years ago by 52k • written 7.5 years ago by ▴ 10
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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 7.5 years ago by 43k • written 7.5 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 7.5 years ago by 43k • written 7.5 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 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
2
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5
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5.9k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 7.6 years ago by 43k • written 7.7 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 7.7 years ago by 43k • written 7.7 years ago by ▴ 90
0
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7
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4.0k
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Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
7.8 years ago Jeff Skinner • 0
3
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19
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4.2k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
7.9 years ago mheydarpour ▴ 10
0
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1
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1.8k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
2
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13
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5.8k
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DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
8.0 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 8.0 years ago by 43k • written 8.0 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 8.3 years ago by ★ 28k • written 8.3 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 8.3 years ago by 52k • written 8.3 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 8.7 years ago by ★ 28k • written 8.7 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 8.7 years ago by 43k • written 8.7 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
8.7 years ago sebastiano.curreli • 0
2
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6
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2.1k
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 8.8 years ago by 43k • written 8.8 years ago by ▴ 10
2
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4
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6.0k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.8 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
9.0 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 9.2 years ago by 43k • written 9.2 years ago by ▴ 60
4
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9
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2.4k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
9.2 years ago vedran.franke • 0
1
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4
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1.5k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
9.3 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 9.3 years ago by 43k • written 9.3 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by kahunroleh • 0
Yes, you can perform DEG analysis across two batches with one shared sample by using batch correction methods like ComBat or limma. These t…
Comment: displaying the differential expression with deseq2 over 4X2 samples with the in by Martijn • 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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