RMA Background Correction
Background correct each column of a matrix
rma.background.correct(x,copy=TRUE)
x |
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. |
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.
A RMA background corrected matrix.
Ben Bolstad, bmbolstad.com
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
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