Showing : Contrasts • reset
3
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3
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645
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 8 months ago by ★ 4.6k • written 8 months ago by ▴ 10
2
votes
3
replies
652
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 10 months ago by 52k • written 10 months ago by • 0
0
votes
3
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1.1k
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 18 months ago by 67k • written 18 months ago by • 0
1
vote
2
replies
760
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
19 months ago jovel_juan ▴ 30
3
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6
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1.5k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.1 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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880
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
3
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8
replies
4.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.7 years ago by ▴ 10
0
votes
3
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1.8k
views
limma voom contrasts
contrasts limma voom
updated 2.9 years ago by 52k • written 2.9 years ago by ▴ 90
0
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1
reply
917
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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2
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1.2k
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.4 years ago James • 0
0
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3
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1.3k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
2
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8
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2.6k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.7 years ago Jane ▴ 10
3
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8
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1.5k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.1 years ago by 67k • written 5.1 years ago by • 0
0
votes
1
reply
1.3k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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0
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854
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.1 years ago ingerslev • 0
0
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1
reply
1.3k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
votes
3
replies
1.6k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 180
0
votes
4
replies
1.2k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.3 years ago by 52k • written 5.3 years ago by • 0
0
votes
1
reply
842
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
3
votes
5
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1.7k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
2
votes
6
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1.4k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.9 years ago by 52k • written 5.9 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: Are unequal sample sizes in differential gene expression (DGE) analysis a proble by Amora • 0
Both edgeR and DESeq2 can handle unequal group sizes if you ensure proper quality control and variance estimation. [sprunki retake][1] …
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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