Showing : Contrasts • reset
3
votes
3
replies
340
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 9 weeks ago by ★ 4.2k • written 9 weeks ago by ▴ 10
2
votes
3
replies
368
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 3 months ago by 51k • written 3 months ago by • 0
0
votes
3
replies
768
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 11 months ago by 66k • written 12 months ago by • 0
1
vote
2
replies
602
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
12 months ago jovel_juan ▴ 30
3
votes
6
replies
1.1k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
18 months ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
702
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 20 months ago by 51k • written 20 months ago by • 0
3
votes
8
replies
3.6k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.2 years ago by ▴ 10
0
votes
3
replies
1.4k
views
limma voom contrasts
contrasts limma voom
updated 2.3 years ago by 51k • written 2.3 years ago by ▴ 90
0
votes
1
reply
774
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
0
votes
2
replies
1.0k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.9 years ago • updated 2.8 years ago James • 0
0
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3
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1.1k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
votes
8
replies
2.2k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.1 years ago Jane ▴ 10
3
votes
8
replies
1.3k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.5 years ago by 66k • written 4.5 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
0
votes
0
replies
714
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.6 years ago ingerslev • 0
0
votes
1
reply
1.2k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.6 years ago by 42k • written 4.6 years ago by ▴ 180
0
votes
4
replies
1.0k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 4.8 years ago by 51k • written 4.8 years ago by • 0
0
votes
1
reply
705
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
3
votes
5
replies
1.5k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 40
2
votes
6
replies
1.2k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.4 years ago by 51k • written 5.4 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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