Showing : Contrasts • reset
3
votes
3
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720
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 9 months ago by ★ 4.7k • written 9 months ago by ▴ 10
2
votes
3
replies
724
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 11 months ago by 52k • written 11 months ago by • 0
0
votes
3
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1.2k
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
2
replies
778
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
20 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
2.2 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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896
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
3
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8
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4.6k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.8 years ago by ▴ 10
0
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3
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1.8k
views
limma voom contrasts
contrasts limma voom
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 90
0
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1
reply
940
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.1 years ago by 43k • written 3.1 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
3.5 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 3.6 years ago by ★ 4.0k • written 3.6 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
3.8 years ago • updated 3.7 years ago Jane ▴ 10
3
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8
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1.6k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
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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 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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0
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872
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.2 years ago ingerslev • 0
0
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1
reply
1.4k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
2
votes
3
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1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.3 years ago by 43k • written 5.3 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 5.4 years ago by 52k • written 5.4 years ago by • 0
0
votes
1
reply
857
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
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5
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1.7k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.9 years ago by ★ 28k • written 5.9 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 6.0 years ago by 52k • written 6.0 years ago by • 0
21 results • Page 1 of 1
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Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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