Showing : contrasts • reset
3
votes
8
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3.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.0 years ago by ▴ 10
3
votes
8
replies
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
2
votes
8
replies
2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago • updated 2.9 years ago Jane ▴ 10
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
3
votes
6
replies
995
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
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
0
votes
4
replies
987
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
3
votes
3
replies
207
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 5 days ago by ★ 4.1k • written 5 days ago by ▴ 10
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.5 years ago by 41k • written 4.5 years ago by ▴ 180
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
1
vote
3
replies
666
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
0
votes
3
replies
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
3
replies
292
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
3
replies
664
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 9 months ago by 65k • written 10 months ago by • 0
0
votes
2
replies
968
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.7 years ago James • 0
1
vote
2
replies
563
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
10 months ago jovel_juan ▴ 30
0
votes
1
reply
730
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
0
votes
1
reply
679
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
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
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
0
votes
0
replies
681
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.4 years ago ingerslev • 0
21 results • Page 1 of 1
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Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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