[BioC] affy package and ST arrays

Hooiveld, Guido Guido.Hooiveld at wur.nl
Tue Dec 14 08:48:50 CET 2010

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.


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 at wur.nl

> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of 
> Michal Blazejczyk
> Sent: Tuesday, December 14, 2010 05:53
> To: bioconductor at 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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