Showing : contrasts • reset
3
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3
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1.1k
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 19 months ago by ★ 5.0k • written 19 months ago by ▴ 10
2
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3
replies
1.1k
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 20 months ago by 53k • written 20 months ago by • 0
0
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3
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1.6k
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
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2
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937
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.5 years ago jovel_juan ▴ 30
3
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6
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1.9k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.0 years ago mohammedtoufiq91 ▴ 10
1
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3
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1.1k
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
3
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8
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5.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.6 years ago by ▴ 10
0
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3
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2.2k
views
limma voom contrasts
contrasts limma voom
updated 3.8 years ago by 53k • written 3.8 years ago by ▴ 90
0
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1
reply
1.1k
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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2
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1.4k
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
4.3 years ago James • 0
0
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3
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1.6k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
2
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8
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3.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.5 years ago Jane ▴ 10
3
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8
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1.9k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
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1
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1.5k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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0
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1.0k
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
6.0 years ago ingerslev • 0
0
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1
reply
1.5k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
3
replies
1.9k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 180
0
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4
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1.6k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
0
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1
reply
1.0k
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
3
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5
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2.0k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 40
2
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6
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1.7k
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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Popular Question to Hervé Pagès 16k
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Popular Question to James W. MacDonald 68k
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