Showing : Contrast • reset
1
vote
2
replies
218
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
0
votes
5
replies
776
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
4
replies
1.2k
views
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
0
votes
3
replies
830
views
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
votes
1
reply
743
views
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
votes
3
replies
1.3k
views
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
votes
1
reply
997
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago • updated 2.7 years ago slcno • 0
7
votes
9
replies
13k
views
Contrasts in DESeq2
deseq2 contrast
updated 20 months ago by • 0 • written 3.6 years ago by ▴ 60
3
votes
2
replies
804
views
LIMMA Time descendant design
limma time-dependant contrast
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 10
5
votes
10
replies
1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
1
vote
1
reply
25k
views
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
0
votes
2
replies
703
views
same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
4
replies
1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.6 years ago luciest.rodriguez • 0
1
vote
3
replies
3.6k
views
Multi-factor analysis Deseq2
deseq2 contrast LTR
5.5 years ago • updated 4.6 years ago Iryna • 0
1
vote
6
replies
1.2k
views
dseq2 results synergy contrast
deseq2 contrast synergy
updated 10 months ago by ▴ 10 • written 4.9 years ago by ▴ 90
0
votes
9
replies
2.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.2 years ago ariel ▴ 20
6
votes
7
replies
1.8k
views
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
votes
5
replies
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
votes
1
reply
903
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 5.4 years ago by 50k • written 5.4 years ago by • 0
0
votes
5
replies
1.4k
views
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
0
votes
3
replies
1.0k
views
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
1
vote
5
replies
2.4k
views
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
4
votes
4
replies
8.0k
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 6.2 years ago by 50k • written 6.3 years ago by ▴ 20
9
votes
1
reply
4.4k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 60
2
votes
4
replies
1.5k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 60
0
votes
4
replies
1.7k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 6.4 years ago by 41k • written 6.8 years ago by • 0
0
votes
2
replies
1.1k
views
Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
2
votes
5
replies
2.4k
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 6.6 years ago by 50k • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.6k
views
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
votes
7
replies
13k
views
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
2
votes
2
replies
2.1k
views
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
votes
5
replies
5.2k
views
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
votes
1
reply
1.4k
views
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
0
votes
7
replies
3.6k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
7.0 years ago Jeff Skinner • 0
3
votes
19
replies
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
votes
1
reply
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
votes
13
replies
4.8k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
7.2 years ago crfitzpat • 0
2
votes
3
replies
1.2k
views
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
0
votes
2
replies
1.1k
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
0
votes
3
replies
1.9k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 7.6 years ago by 50k • written 7.6 years ago by ▴ 20
2
votes
6
replies
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
vote
6
replies
1.2k
views
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
votes
2
replies
2.1k
views
"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
votes
6
replies
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
votes
4
replies
5.4k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.1 years ago dwzhang.wisc ▴ 20
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago • updated 8.2 years ago rclaire ▴ 20
6
votes
1
reply
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
votes
9
replies
2.1k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
8.4 years ago vedran.franke • 0
1
vote
4
replies
1.4k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
8.5 years ago arrigonialberto86 • 0
0
votes
1
reply
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
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Awards • All
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Locations • All
Canada, 7 minutes ago
France, 12 minutes ago
UPF, Barcelona, Spain, 15 minutes ago
United States, 28 minutes ago
Belgium, 52 minutes ago
Traffic: 971 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6