pcaBeforeCorrection: PCA before correction.
In syspremed/exploBATCHSerial: Explore batch effect (exploBATCH) is a package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2016).

PCA before correction.

1	pcaBeforeCorrection(rs1, grps, cGsub, batchCL, Conf, type, Ys)

`rs1`	Results of PCA.
`grps`	Number of batches.
`cGsub`	Colors
`batchCL`	A vector identifying batches.
`Conf`	A vector identifying biological classes.
`type`	Names biological classes.
`Ys`	Expression data.

PCA before correction

Results in the pcaBeforeCorrection folder in the working directory.

Gift Nyamundanda and Anguraj Sadanandam

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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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

syspremed/exploBATCHSerial documentation built on May 20, 2019, 8:33 a.m.

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