[BioC] liimma and Across Array Normalisation

[Gordon K Smyth]

If 'x' is your background-corrected EList, then

   w <- rep(1,nrow(x))
   w[controls] <- 100
   y <- normalizeBetweenArrays(x, method="cyclicloess", weights=w)

does what you want.

For an example of this approach:

   http://rnajournal.cshlp.org/content/19/7/876

Best wishes
Gordon

--------- original message ----------
Saket Choudhary saketkc at gmail.com
Thu Feb 6 06:59:42 CET 2014

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

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