[BioC] liimma and Across Array Normalisation

[Saket Choudhary]

I am analysing a proteomics microarray data set for a two group
sample(Normal and Disease) using single color channel. The arrays have
a set of pre-defined CONTROL points whose expression levels are
supposed to be similar/same across all the arrays.

I would like to 'normalise' the levels of all probes such that
normalisation ends up with all CONTROL points having similar
expression levels. If I understand it right, normalizebetweenarray
does not allow this kind of normalisation.

Is there a pre-implemented function to do this? If not, what would be
a way to acheive this kind of normalisation?

Code: https://gist.github.com/saketkc/8669586