Batch correction of joint SAGA data sets.

saga_batch removes batch effects from the joint data set. For each sample, the user must specify a batch number in the "SAGA_USER_Samples.txt" file. If no batch numbers are available - you'll still have to provide a number for the samples. You can use any integer number beginning with 1. The batch correction of the data set relies on the ComBat algorithm/package.

saga_batch(
  matrix.SAGA.qn,
  matrix.test.qn,
  rawdata,
  pData.joint,
  plotnumber = 2
)

Arguments

matrix.SAGA.qn	quantile normalized saga matrix
matrix.test.qn	quantile normalized test matrix
rawdata	SAGA raw data
pData.joint	matrix with combined SAGA data and user samples.
plotnumber	default=2 for PCA plot with samples in black; alternative: 1 for t-SNE plot

Value

eset.batch batch corrected data set.