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 12 months ago by ★ 4.8k • written 12 months ago by ▴ 10
2
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3
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820
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 13 months ago by 52k • written 13 months ago by • 0
0
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3
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1.3k
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 21 months ago by 68k • written 21 months ago by • 0
1
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2
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814
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
22 months ago jovel_juan ▴ 30
3
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6
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1.6k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.4 years ago mohammedtoufiq91 ▴ 10
1
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3
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932
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
3
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8
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4.9k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.0 years ago by ▴ 10
0
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3
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1.9k
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limma voom contrasts
contrasts limma voom
updated 3.1 years ago by 52k • written 3.1 years ago by ▴ 90
0
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1
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972
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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2
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1.3k
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.7 years ago James • 0
0
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3
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1.4k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
2
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8
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2.7k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.9 years ago Jane ▴ 10
3
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8
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1.7k
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Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
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1
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1.3k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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0
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896
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.4 years ago ingerslev • 0
0
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1
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1.4k
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
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3
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1.7k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 180
0
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4
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1.3k
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Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.6 years ago by 52k • written 5.6 years ago by • 0
0
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1
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884
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
3
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5
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1.8k
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 40
2
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6
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1.5k
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.2 years ago by 52k • written 6.2 years ago by • 0
21 results • Page 1 of 1
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Replies
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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