Showing : Contrasts • reset
2
votes
3
replies
284
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
3
replies
651
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
vote
2
replies
558
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
10 months ago jovel_juan ▴ 30
3
votes
6
replies
981
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
661
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 18 months ago by 50k • written 18 months ago by • 0
3
votes
8
replies
3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 24 months ago by ▴ 10
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts limma voom
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 90
0
votes
1
reply
719
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
votes
2
replies
962
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.7 years ago James • 0
0
votes
3
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1.0k
views
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
votes
8
replies
2.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
3
votes
8
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1.2k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
0
votes
1
reply
1.0k
views
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
votes
0
replies
676
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.4 years ago ingerslev • 0
0
votes
1
reply
1.1k
views
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
votes
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
977
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
676
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
replies
1.4k
views
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
replies
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
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Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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