Showing : Contrasts • reset
2
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3
replies
271
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
3
replies
634
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
1
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2
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547
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
10 months ago jovel_juan ▴ 30
3
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6
replies
972
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
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3
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654
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 17 months ago by 50k • written 17 months ago by • 0
3
votes
8
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3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 23 months ago by ▴ 10
0
votes
3
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1.3k
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limma voom contrasts
contrasts limma voom
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 90
0
votes
1
reply
710
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
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2
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953
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.6 years ago James • 0
0
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3
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990
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
2
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8
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2.0k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
3
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8
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1.2k
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Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
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1
reply
1.0k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
0
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0
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670
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.4 years ago ingerslev • 0
0
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1
reply
1.1k
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
2
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3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 180
0
votes
4
replies
967
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 4.6 years ago by 50k • written 4.6 years ago by • 0
0
votes
1
reply
670
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
3
votes
5
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1.4k
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
2
votes
6
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1.1k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
20 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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