A matrix of intensities where each column corresponds to a
chip and each row is a probe.
copy
Make a copy of matrix before background correctiong. Usually safer to
work with a copy, but in certain situations not making a copy of the
matrix, but instead background correcting it in place will be more memory friendly.
Value
A RMA background corrected matrix.
Details
Assumes PMs are a convolution of normal and exponentional. So we
observe X+Y where X is backround and Y is signal. bg.adjust
returns E[Y|X+Y, Y>0] as our backround corrected
PM.
References
Bolstad, BM (2004) Low Level Analysis of High-density
Oligonucleotide Array Data: Background, Normalization and
Summarization. PhD Dissertation. University of California,
Berkeley. pp 17-21