Showing : contrasts • reset
3
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3
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 7 months ago by ★ 4.6k • written 7 months ago by ▴ 10
2
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3
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583
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 months ago by 52k • written 8 months ago by • 0
0
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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 17 months ago by 67k • written 17 months ago by • 0
1
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2
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729
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
18 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
24 months ago mohammedtoufiq91 ▴ 10
1
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3
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849
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
3
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8
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4.3k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.6 years ago by ▴ 10
0
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3
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1.7k
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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
891
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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2
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1.1k
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.3 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 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
2
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8
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2.5k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.5 years ago Jane ▴ 10
3
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8
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1.5k
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Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.0 years ago by 67k • written 5.0 years ago by • 0
0
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1
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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 5.0 years ago by 43k • written 5.0 years ago by • 0
0
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0
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831
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.0 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 5.0 years ago by 43k • written 5.0 years ago by • 0
2
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3
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1.6k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 180
0
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4
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1.2k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.2 years ago by 52k • written 5.2 years ago by • 0
0
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1
reply
822
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
3
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5
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1.7k
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 40
2
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6
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1.3k
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.8 years ago by 52k • written 5.8 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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