[BioC] Problem with MAS5 calls on MoEx array

[cstrato]

Dear Peter,

Please note that exon arrays have only PM probesets and no MM probesets, 
thus usually it is not possible to do mas5 with these arrays.

As far as I know my BioC package "xps" is the only package where you can 
indeed apply mas5 to exon arrays.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


Peter Saffrey wrote:
> I am using the affy library with mouseexonpmcdf to compute RMA and MAS5 calls.
> The RMA works fine. The MAS5 throws errors:
>
>   
>> library("affy")
>>     
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>   
>> adata <- ReadAffy()
>> adata at cdfName <- "mouseexonpmcdf"
>> pmaCalls <- mas5(adata)
>>     
> background correction: mas 
> PM/MM correction : mas 
> expression values: mas 
> background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign
> function call (arg 1)
>   
>> sessionInfo()
>>     
> R version 2.9.2 (2009-08-24) 
> x86_64-pc-linux-gnu 
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] mouseexonpmcdf_1.1 affy_1.22.1        Biobase_2.4.1     
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0        preprocessCore_1.6.0 tools_2.9.2         
>
>
> My CEL file can be found here:
>
> http://cs-analysis.clinmed.gla.ac.uk/MoEx/KC4MoEX1E143.CEL
>
> Peter
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>