Showing : contrasts • reset
3
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3
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629
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 8 months ago by ★ 4.6k • written 8 months ago by ▴ 10
2
votes
3
replies
632
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
3
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1.1k
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 18 months ago by 67k • written 18 months ago by • 0
1
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2
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749
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
19 months ago jovel_juan ▴ 30
3
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6
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1.4k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.1 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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869
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
3
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8
replies
4.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.7 years ago by ▴ 10
0
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3
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1.8k
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limma voom contrasts
contrasts limma voom
updated 2.8 years ago by 52k • written 2.8 years ago by ▴ 90
0
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1
reply
911
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.9 years ago by 43k • written 2.9 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
3.4 years ago James • 0
0
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3
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1.3k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
2
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8
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2.5k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.6 years ago Jane ▴ 10
3
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8
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1.5k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.1 years ago by 67k • written 5.1 years ago by • 0
0
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1
reply
1.2k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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0
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848
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.1 years ago ingerslev • 0
0
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1
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1.3k
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
votes
3
replies
1.6k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 180
0
votes
4
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1.2k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.3 years ago by 52k • written 5.3 years ago by • 0
0
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1
reply
835
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
3
votes
5
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1.7k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
2
votes
6
replies
1.4k
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.9 years ago by 52k • written 5.9 years ago by • 0
21 results • Page 1 of 1
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Replies
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…
Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k
I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k
I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…
Votes
Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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