Showing : contrasts • reset
0
votes
3
replies
419
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 5 months ago by 64k • written 5 months ago by • 0
1
vote
2
replies
381
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
6 months ago jovel_juan ▴ 30
3
votes
6
replies
713
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
12 months ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
512
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 13 months ago by 49k • written 13 months ago by • 0
3
votes
8
replies
2.8k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 19 months ago by ▴ 10
0
votes
3
replies
1.1k
views
limma voom contrasts
contrasts limma voom
updated 21 months ago by 49k • written 21 months ago by ▴ 90
0
votes
1
reply
611
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 22 months ago by 41k • written 22 months ago by • 0
0
votes
2
replies
837
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.3 years ago James • 0
0
votes
3
replies
836
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.3 years ago by 3.9k • written 2.3 years ago by • 0
2
votes
8
replies
1.7k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.6 years ago • updated 2.5 years ago Jane • 0
3
votes
8
replies
1.0k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.0 years ago by 64k • written 4.0 years ago by • 0
0
votes
1
reply
853
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
0
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0
replies
579
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.0 years ago ingerslev • 0
0
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1
reply
1.0k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
2
votes
3
replies
1.2k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 180
0
votes
4
replies
851
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 4.2 years ago by 49k • written 4.2 years ago by • 0
0
votes
1
reply
593
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
3
votes
5
replies
1.3k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 40
2
votes
6
replies
979
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 4.8 years ago by 49k • written 4.8 years ago by • 0
19 results • Page 1 of 1
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Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change by James W. MacDonald 64k
You could look at my answer and extrapolate from there.
Comment: enrichGOgradient color change by WU • 0
I would like to ask how to make the counts legend black. Thank you.
Answer: Problems with FLOWAI by Alexander • 0
Hi. The length of the file path, or whether the files are local on the computer has nothing to do with it in my experience. I watched the a…
Answer: Asses fit of variance prior by Gordon Smyth 49k
> is it advisable to asses the fit of the variance prior before running limma? No, neither necessary nor possible. If this sort of checki…
Votes
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
How to know if I should use voomWithQualityWeights() or not?
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