Showing : Contrast • reset
17
votes
7
replies
13k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 10
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 42k • written 6.4 years ago by ▴ 60
8
votes
9
replies
4.4k
views
DESeq2: Compare expression of one group to the mean of others
deseq2 heterosis contrast design and contrast matrix
updated 8.9 years ago by 42k • written 8.9 years ago by ▴ 10
7
votes
9
replies
13k
views
Contrasts in DESeq2
deseq2 contrast
updated 21 months ago by • 0 • written 3.6 years ago by ▴ 60
6
votes
2
replies
4.8k
views
All same padj of contrast results in the DESeq2
deseq2 padj contrast results
updated 8.8 years ago by 42k • written 8.8 years ago by ▴ 20
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.5 years ago by 42k • written 8.5 years ago by ▴ 60
6
votes
7
replies
1.8k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 5.3 years ago by 42k • written 5.3 years ago by ▴ 30
5
votes
11
replies
11k
views
DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 9.2 years ago by 42k • written 9.2 years ago by ▴ 90
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 42k • written 3.9 years ago by • 0
4
votes
4
replies
8.1k
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 6.3 years ago by 50k • written 6.3 years ago by ▴ 20
4
votes
9
replies
2.1k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
8.5 years ago vedran.franke • 0
3
votes
5
replies
1.5k
views
pass limma contrast matrix variable
contrast limma
updated 8.6 years ago by 50k • written 8.6 years ago by ▴ 210
3
votes
5
replies
1.5k
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 10
3
votes
2
replies
818
views
LIMMA Time descendant design
limma time-dependant contrast
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 10
3
votes
16
replies
4.1k
views
limma contrast matrix
limma contrast design and contrast matrix
9.5 years ago Smith H. ▴ 20
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
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
8.0 years ago sebastiano.curreli • 0
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
2
votes
6
replies
3.3k
views
voom/limma contrast for comparing one level against base-line
limma voom contrast
updated 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 80
2
votes
8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.9 years ago shao ▴ 100
2
votes
3
replies
1.3k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago rclaire ▴ 20
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
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 8.1 years ago by 42k • written 8.1 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 6.7 years ago by 50k • written 6.7 years ago by ▴ 10
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
2
votes
3
replies
1.2k
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 7.3 years ago by 42k • written 7.3 years ago by • 0
2
votes
13
replies
4.9k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
7.2 years ago crfitzpat • 0
2
votes
1
reply
918
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 5.5 years ago by 50k • written 5.5 years ago by • 0
2
votes
5
replies
5.3k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
2
votes
2
replies
2.1k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 6.9 years ago by ★ 28k • written 6.9 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
1
vote
4
replies
1.4k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
8.6 years ago arrigonialberto86 • 0
1
vote
6
replies
1.3k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 8.0 years ago by 42k • written 8.0 years ago by ▴ 90
1
vote
3
replies
3.6k
views
Multi-factor analysis Deseq2
deseq2 contrast LTR
5.6 years ago • updated 4.7 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 5.0 years ago by ▴ 90
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 42k • written 4.3 years ago by ★ 1.5k
1
vote
2
replies
249
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
8 weeks ago • updated 7 weeks ago Chanderkant Chaudhary • 0
0
votes
5
replies
1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.7 years ago by 42k • written 5.7 years ago by ▴ 10
0
votes
5
replies
819
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 11 months ago by 65k • written 11 months 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 42k • 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()
7.1 years ago Jeff Skinner • 0
0
votes
1
reply
1.6k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 7.2 years ago by 42k • written 7.2 years ago by • 0
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
0
votes
3
replies
850
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
19 months ago Edgar • 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
0
votes
2
replies
714
views
same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
4
replies
1.3k
views
Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 15 months ago by ▴ 780 • written 15 months 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
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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