Showing : contrast matrix • reset
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Designating contrasts in diffSpliceDGE to test for nested effects
diffSpliceDGE Contrast matrix edger
updated 11 months ago by 43k • written 11 months ago by • 0
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 17 months ago by 43k • written 18 months ago by • 0
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Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 3.0 years ago by 58k • written 3.0 years ago by ▴ 230
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Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
4.0 years ago stinehedensted • 0
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differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix
updated 4.2 years ago by 7.6k • written 4.2 years ago by • 0
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2
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Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 4 months ago by • 0 • written 4.2 years ago by ▴ 20
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Syntax of DESeq2 contrast argument for all pairwise comparisons
deseq2 contrast matrix
updated 4.6 years ago by 34k • written 4.6 years ago by • 0
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7
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Design matrix and contrast for RNA knockdown experiment
design matrix limma contrast matrix
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ▴ 140
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What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger limma model.matrix contrast matrix design matrix
updated 5.2 years ago by ▴ 590 • written 5.2 years ago by • 0
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Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Comment: "full model matrix is less than full rank" by fernandogs97 • 0
Hello ATpoint, thank you very much for your fast and helpful response, finally I corrected the error by changing the separator, instead of …
Comment: unable to load shared object Rsamtools.dll': by Mike Smith ★ 5.1k
Can you include the command you're running (I guess it's `BiocManager::install("Rsamtools", type = "source")` )? It would also be useful to…
Comment: unable to load shared object Rsamtools.dll': by franck.richard • 0
Finally, I only encounter this problem with Rsamtools. It works fine with the other packages. Thank you for your help!
Comment: Unique GPos taking into account mcols by maltethodberg ▴ 140
Yes, I managed to find those functions via the VariantAnnotation package. The "Quad" versions are very handy for matching seqnames/pos/effe…
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Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
Comment: deseq2 machine sizing best practices for very large data set
Comment: Warning messages on Apple M1 BigSur
Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset
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