Bioconductor Batch Correction

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2.0k

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scrna-seq integration batch correction

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by p.joshi ▴ 40

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1.4k

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methylation ComBat Linear models batch correction AIC

updated 5.3 years ago by Kevin Blighe ★ 4.0k • written 5.3 years ago by lucasmiranda42 • 0

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840

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DESeq2 batch correction

updated 5.4 years ago by James W. MacDonald 68k • written 5.4 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.6 years ago by Rory Stark ★ 5.2k • written 5.6 years ago by rm1238 • 0

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1.2k

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deseq2 differential expression batch correction design

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by wunderl ▴ 40

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1.8k

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deseq2 differential expression batch correction

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by wunderl ▴ 40

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2.3k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.0 years ago by Vladimir Kiselev ▴ 150 • written 6.0 years ago by hamza_karakurt ▴ 60

7 results • Page 1 of 1

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Answer: best way to grouping GSM belonging to different datasets (with different platfor by James W. MacDonald 68k

The only defensible way is to make comparisons within experiments and then do a meta-analysis. But that assumes you have identified multipl…

Comment: DESeq2 estimateSizeFactors with control genes by sofia.rigou • 0

I am also trying to use this function to estimate sizefactor based on RT-dPCR data but estimateSizeFactor only takes integers. Should I mul…

Comment: DiffBind custom normalization factor by Abbie • 0

Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k

All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…

Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…

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clusterProfiler-GO enrichment Error

A: Machine learning in R book

Data preparation and Machine learning on time course RNAseq data

Answer: Use of org.Rn.eg.db with GRCr8 reference genome

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