Hey, Michal -

Perhaps try norm.type='pmonly' n the call to justPlier()?

Cordially,

- Jeremy


On Mon, Dec 13, 2010 at 11:48 PM, Hooiveld, Guido <Guido.Hooiveld@wur.nl>wrote:

> Hi Michal,
>
> These functions will never work because the ST arrays do not contain any
> mismatch probes, which are required for MAS5, GCRMA and PLIER. In other
> words, these are PM (perfect match) only arrays that can be normalized with
> e.g. RMA or VSN.
>
> HTH,
> Guido
>
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com
> email:      guido.hooiveld@wur.nl
>
>
>
> > -----Original Message-----
> > From: bioconductor-bounces@r-project.org
> > [mailto:bioconductor-bounces@r-project.org] On Behalf Of
> > Michal Blazejczyk
> > Sent: Tuesday, December 14, 2010 05:53
> > To: bioconductor@r-project.org
> > Subject: [BioC] affy package and ST arrays
> >
> > Dear list,
> >
> > I have a question.  I've noticed that The most recent
> > Biocinductor version contains CDF packages for Affymetrix's ST arrays.
> >
> > As a result, functions such as rma() or just.rma() now work
> > well with these arrays, which is great.
> >
> > However, many other normalization functions (e.g. gcrma(),
> > mas5(), mas5calls.AffyBatch(), or justPlier()) are still
> > throwing errors.
> >
> > Does anybody know if there are plans to make these other
> > methods work with the CDF packages for ST arrays?
> >
> > Best regards,
> >
> > Michal Blazejczyk
> > FlexArray Lead Developer
> > McGill University and Genome Quebec Innovation Centre
> > 514-398-4400 x09625 http://genomequebec.mcgill.ca/FlexArray
> >
> > _______________________________________________
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> >
> >
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-- 
Jeremy Gollub
jeremy@gollub.net

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