[BioC] VSN exclusion of probes

[Hans-Ulrich Klein]

Dear All,

I want to normalize two-color oligo-arrays with the VSN method. The 
arrays contain some blank spots, which have a much stronger dye bias 
than the oligo spots. Therefore, I do not want them to be used by the 
LTS for parameter estimation. However, they should be normalized after 
parameter estimation.

I tried the following code:
(RG is a RGList object holding the Raw data)

RG <- backgroundCorrect(RG, method="subtract");
y <- cbind(RG$G, RG$R);
subSet <- RG$genes$Status != "blank";   # exclude blank spots
vsnres <- vsn(y[subSet, ], strata=RG$genes$Block[subSet]);
pars <- preproc(description(vsnres))$vsnParams;
y <- vsnh(y, pars, strata=RG$genes$Block);


The last statement leads to this error message:
Error in vsnh(y, pars, strata = RG$genes$Block) :
    Invalid argument 'e_y', must be a real matrix.


What is wrong with my code? What is 'e_y'?

Is there a convenient way to use weights (e.g. stored in 
RG$genes$weights)  for parameter estimation? It would be nice to exclude 
only the k-th probe on array i and not the k-th probe of all arrays (as 
done above).

Regards,
Hans-Ulrich

-- 
Westfälische Wilhelms-Universität Münster
Department of Medical Informatics and Biomathematics
Hans-Ulrich Klein, Domagkstr. 9 (Raum 27), 48149 Münster