Question: How to eliminate batch effect using removeBatchEffect function for tissue expression profiles?
0
gravatar for rice.researcher
23 months ago by
Korea, Republic Of
rice.researcher150 wrote:

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)
limma microarray batch-effect R • 939 views
ADD COMMENTlink modified 23 months ago by zx87549.7k • written 23 months ago by rice.researcher150
1

i'd rather suggest BatchQC for batch effect removal + visualization + statistics https://bioconductor.org/packages/release/bioc/html/BatchQC.html

ADD REPLYlink written 23 months ago by lessismore930
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