Character, the full path to the input files, which must be either "x.txt" and "y.txt" or "x.filt.txt" and "y.filt.txt".
snps
Data.frame, with three columns containing SNP ID, chromosome and Mb location in that order. May be obtained from ftp://ftp.jax.org/MUGA.
x1
Numeric matrix containing X intensities for batch 1 containing samples in rows and markers in columns. Number of samples should be larger than x2.
y1
Numeric matrix containing Y intensities for batch 1 containing samples in rows and markers in columns. Number of samples should be larger than y2.
x2
Numeric matrix containing X intensities for batch 2 containing samples in rows and markers in columns.
y2
Numeric matrix containing Y intensities for batch 2 containing samples in rows and markers in columns.
Value
FALSEor batch.normalize: returns value is returned. The batch normalized intensities are written to "x.filt.batch.norm.txt" and "y.filt.batch.norm.txt".FALSEor quantilenorm: returns normalized X and Y values for batch 2.
Details
quantile.norm adjusts the intensities of samples in batch 2 to those of batch 1. The number of samples in batch 1 should be greater than the number of samples in batch 2. At each SNP, we form quantiles of the X1 (or Y1) intensity distribution, discarding the upper and lower 0.01