Showing : contrasts • reset
3
votes
3
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759
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 10 months ago by ★ 4.7k • written 10 months ago by ▴ 10
2
votes
3
replies
754
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 11 months ago by 52k • written 11 months ago by • 0
0
votes
3
replies
1.2k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 20 months ago by 68k • written 20 months ago by • 0
1
vote
2
replies
789
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
21 months ago jovel_juan ▴ 30
3
votes
6
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1.5k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.2 years ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
905
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
3
votes
8
replies
4.6k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.8 years ago by ▴ 10
0
votes
3
replies
1.8k
views
limma voom contrasts
contrasts limma voom
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 90
0
votes
1
reply
949
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
replies
1.2k
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.5 years ago James • 0
0
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3
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1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
2
votes
8
replies
2.6k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.8 years ago Jane ▴ 10
3
votes
8
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1.6k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
1
reply
1.3k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
votes
0
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880
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.2 years ago ingerslev • 0
0
votes
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 5.3 years ago by 43k • written 5.3 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 5.4 years ago by 52k • written 5.4 years ago by • 0
0
votes
1
reply
862
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
5
replies
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
replies
1.4k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.0 years ago by 52k • written 6.0 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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