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iDEP-SDSU / idep

Integrated Differential Expression and Pathway analysis
http://ge-lab.org/idep
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Add batch effect removal step? #18

Open gexijin opened 6 years ago

gexijin commented 6 years ago

Some R packages like sva can detect and remove batch effects from RNA-seq data.

https://github.com/iscb-dc-rsg/2016-summer-workshop/tree/master/3B-Hughitt-RNASeq-Coex-Network-Analysis/tutorial https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf

gexijin commented 6 years ago

SVA and Combat are two methods for batch effect removal. http://bioconductor.org/packages/release/bioc/html/sva.html