[BioC] help in arrayMagic?

[pmt1rew at leeds.ac.uk]

Dear all

I have a set of raw data values, 2 channels and 3 hybridisations.  I have
created an array of dimension 474x2x3 and am now trying to normalise the data,
each hybridistaion separately.  I have installed the arrayMagic package and
used the command

>
eSRG<-normalise(arrayDataobject,method="vsn",hybridisationGroups="slideBySlide",spotIdentifier="Name")

which returns the following error message

 begin of normalisation
 the following hybridisation index(es) are used in normalisation step 1 :
1
 vsn normalisation
vsn: 474 x 2 matrix (1 stratum). Please wait for 10 dots: ..........
 the following hybridisation index(es) are used in normalisation step 2 :
2
 vsn normalisation
vsn: 474 x 2 matrix (1 stratum). Please wait for 10 dots: ......Error: L-BFGS-B
needs finite values of fn


My data matrix contains no zeros or negative values or Inf and there are are no
coloumns which contain all the same value.  Hope that you can help with why and
how to amend it?

Furthermore, I have a column of 474 gene names.  They are non-unique since I
have six replicates per gene.  Thus I have used used spotIdentifier = "Name"
which is one of my column names.  I get the line

non-unique identifiers found in getSpotAttr(arrayDataObject)
no spot/gene names have been added to the exprSetRG in normalise

however when I call qPL anything to do with replicate spot returns a value of
NA?

Hope you can help.  Thanks

Rebecca