[BioC] help in arrayMagic?

[Andreas Buness]

Dear Rebecca,

the error 'L-BFGS-B' is related to the normalisation method 'vsn'
and your specific data set. So e.g., if using 'loess' instead, the
error would not occur. Otherwise possibly change the options, e.g.
skip the argument 'hybridisationGroups' or specify 'pstart' for 'vsn'
in the function call of 'normalise'. cf. the discussion in

https://stat.ethz.ch/pipermail/ bioconductor/2004-May/004738.html
https://stat.ethz.ch/pipermail/ bioconductor/2004-June/005076.html

Non-unique identifiers cannot be used to label matrix rows without
ambiguity. But the call of 'qualityParameters' with argument
'spotIdentifier="Name"' as specified in the vignette should
give you results regarding your replicate spots.

Hope this helps, best regards
Andreas



pmt1rew at leeds.ac.uk wrote:
> 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
> 
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-- 
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Andreas Buness
Molecular Genome Analysis (B050)
German Cancer Research Center          room          TP3 2.109
Im Neuenheimer Feld 580                phone ++49 6221 42-4716
D-69120 Heidelberg
Germany

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