Bioconductor Batch Correction

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.5 years ago by Vladimir Kiselev ▴ 150 • written 5.5 years ago by hamza_karakurt ▴ 60

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1.6k

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deseq2 differential expression batch correction

updated 5.3 years ago by Michael Love 42k • written 5.3 years ago by wunderl ▴ 40

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1.1k

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deseq2 differential expression batch correction design

updated 5.3 years ago by Michael Love 42k • written 5.3 years ago by wunderl ▴ 40

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1.1k

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Diffbind ATAC batch correction blocking factor

updated 5.2 years ago by Rory Stark ★ 5.2k • written 5.2 years ago by rm1238 • 0

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742

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DESeq2 batch correction

updated 4.9 years ago by James W. MacDonald 67k • written 4.9 years ago by MT ▴ 10

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1.2k

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methylation ComBat Linear models batch correction AIC

updated 4.8 years ago by Kevin Blighe ★ 4.0k • written 4.9 years ago by lucasmiranda42 • 0

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1.8k

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scrna-seq integration batch correction

updated 4.7 years ago by Aaron Lun ★ 28k • written 4.7 years ago by p.joshi ▴ 40

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Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10

I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…

Answer: featureCounts fails to load annotation file by James W. MacDonald 67k

I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…

Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k

That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …

Comment: Are transformed values from rlog /vst log2 normalized counts? by James W. MacDonald 67k

The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …

Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10

Many thanks for you detailed answer, I really appreciate it. Could you give me an example (or more if possible) of analysis using count-b…

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Answer: Are transformed values from rlog /vst log2 normalized counts?

Comment: Are transformed values from rlog /vst log2 normalized counts?

Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable

Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical

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Scholar to James W. MacDonald 67k