How to eliminate batch effect using removeBatchEffect function for tissue expression profiles?
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2.4 years ago

For meta-analysis work, I would like to combine two rice GEO series( GSE27988 and GSE27856 ) where each series analyze multiple anatomical tissue related expression profiles.To eliminate batch effect, I'm not sure whether I can use limma removeBatchEffect function as given below. Similar posts I see related to batch effect are generally control vs treatment.

libraray(limma)

batch <- c("A","A","A",... "B","B","B")  # 24 samples in batch A and 14 samples in batch B
corrected<- removeBatchEffect(data, batch)
Microarray batch-effect R limma • 1.4k views
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i'd rather suggest BatchQC for batch effect removal + visualization + statistics https://bioconductor.org/packages/release/bioc/html/BatchQC.html

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