Showing : contrasts • reset
3
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3
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821
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 11 months ago by ★ 4.8k • written 11 months ago by ▴ 10
2
votes
3
replies
793
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 12 months ago by 52k • written 12 months ago by • 0
0
votes
3
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1.3k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
2
replies
802
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
22 months ago jovel_juan ▴ 30
3
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6
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1.6k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.3 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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920
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
3
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8
replies
4.8k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.9 years ago by ▴ 10
0
votes
3
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1.9k
views
limma voom contrasts
contrasts limma voom
updated 3.1 years ago by 52k • written 3.1 years ago by ▴ 90
0
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1
reply
965
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.2 years ago by 43k • written 3.2 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
3.6 years ago James • 0
0
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3
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1.4k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
2
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8
replies
2.7k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.9 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 5.3 years ago by 68k • written 5.3 years ago by • 0
0
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1
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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 5.3 years ago by 43k • written 5.3 years ago by • 0
0
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0
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889
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.3 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 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
3
replies
1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 180
0
votes
4
replies
1.3k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.5 years ago by 52k • written 5.5 years ago by • 0
0
votes
1
reply
876
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
3
votes
5
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1.8k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 40
2
votes
6
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1.5k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
21 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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