Description Details Author(s) References See Also Examples
It contains R scripts for performing formal statistical tests to diagnose batch effect in large scale genomic datasets, and correct for batch effect using an approach detailed in Nyamundanda et al (2016), which is based on the PPCCA model,in large scale genomic datasets. License: What license is it under?
The DESCRIPTION file:
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Explore batch effect (exploBATCH) is an R package for perfoming formal statistical tests to discover and correct batch effect. It searches for directions in the principal subspace that are associated with the batch variable of interest and correct for batch effect by subtracting this
effect only in the affected dimensions. Both the corrected and uncorrected dimensions are then used to predict the data.
Gift Nyamundanda gift.nyamundanda@icr.ac.uk
Maintainer: Gift Nyamundanda <gift.nyamundanda@icr.ac.uk>
Nyamundanda, G. and Sadanandam, A., 2016. A novel and robust statistical method to diagnose and correct batch effects in large-scale genomic data.
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1 2 3 4 5 | ## help(exploBATCH)
## Expression data and batch effect variable is required for this function.
data(Breast)
data(batchBreast)
expBATCH(D= Breast,batchBreast,Conf=NA,mindim=1,maxdim=10,method="ppcca")
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