Bioconductor Batch correction

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1.8k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.1 years ago by Vladimir Kiselev ▴ 150 • written 5.1 years ago by hamza_karakurt ▴ 50

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1.3k

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deseq2 differential expression batch correction

updated 4.9 years ago by Michael Love 41k • written 4.9 years ago by wunderl ▴ 40

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997

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deseq2 differential expression batch correction design

updated 4.9 years ago by Michael Love 41k • written 4.9 years ago by wunderl ▴ 40

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944

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.2k • written 4.7 years ago by rm1238 • 0

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611

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DESeq2 batch correction

updated 4.5 years ago by James W. MacDonald 65k • written 4.5 years ago by MT ▴ 10

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973

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methylation ComBat Linear models batch correction AIC

updated 4.4 years ago by Kevin Blighe ★ 3.9k • written 4.4 years ago by lucasmiranda42 • 0

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1.5k

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scrna-seq integration batch correction

updated 4.3 years ago by Aaron Lun ★ 28k • written 4.3 years ago by p.joshi ▴ 40

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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0

Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…

Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

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Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

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