Bioconductor Cma

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1.3k

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Classification CMA Classification CMA

updated 9.2 years ago by Sean Davis 21k • written 9.2 years ago by Guest User ★ 12k

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804

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CMA CMA

9.9 years ago Guest User ★ 12k

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1.4k

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CMA DiffBind CMA DiffBind

11.1 years ago Paolo Kunderfranco ▴ 350

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870

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Cancer CMA DiffBind Cancer CMA DiffBind

updated 11.2 years ago by Gordon Brown ▴ 70 • written 11.2 years ago by Paolo Kunderfranco ▴ 350

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901

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CMA DiffBind CMA DiffBind

updated 11.2 years ago by Gordon Brown ▴ 70 • written 11.2 years ago by Paolo Kunderfranco ▴ 350

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1.2k

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lumi CMA lumi CMA

updated 11.2 years ago by Moshe Olshansky ▴ 260 • written 11.2 years ago by Paolo Kunderfranco ▴ 350

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863

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Microarray CMA Microarray CMA

updated 12.3 years ago by Tim Triche ★ 4.2k • written 12.3 years ago by Clara Pons ▴ 30

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2.2k

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Microarray Classification limma CMA Microarray Classification limma CMA

12.6 years ago Santosh Patnaik ▴ 30

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762

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CMA CMA

13.4 years ago Mike Dewar ▴ 60

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1.1k

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Classification CMA Classification CMA

13.7 years ago Javier Pérez Florido ▴ 840

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908

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CMA CMA

updated 13.9 years ago by Vincent J. Carey, Jr. 6.7k • written 13.9 years ago by Paul Shannon ★ 1.1k

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933

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Classification CMA Classification CMA

updated 13.9 years ago by Stephen Henderson ▴ 10 • written 13.9 years ago by Juan C Oliveros Collazos ▴ 190

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1.4k

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Microarray Classification Regression limma CMA Microarray Classification Regression limma

14.6 years ago Renaud Gaujoux ▴ 170

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845

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CMA CMA

updated 14.6 years ago by Patrick Aboyoun 1.6k • written 14.6 years ago by Ortiz, Maria ▴ 10

14 results • Page 1 of 1

Recent ...

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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k

Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.

Comment: collapseReplicates error after tximeta by Michael Love 40k

A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…

Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Votes

Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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