[BioC] Problem with MAS5 calls on MoEx array

[Peter Saffrey]

Hi,

Thanks for the recommendation. This seems to bring its own problems. Here is the error from trying to install xps.

g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/include/root -c XPSUtils.cxx
XPSUtils.cxx: In function 'void READ_WSTRING(std::ifstream&, char*&, Bool_t)':
XPSUtils.cxx:4611: error: 'wcstombs' was not declared in this scope
make: *** [XPSUtils.o] Error 1
ERROR: compilation failed for package 'xps'

$ uname -a
Linux cs-analysis 2.6.31-17-generic #54-Ubuntu SMP Thu Dec 10 17:01:44 UTC 2009 x86_64 GNU/Linux
$ gcc --version
gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1

Cheers,

Peter

________________________________________
From: cstrato [cstrato at aon.at]
Sent: 08 February 2010 21:44
To: Peter Saffrey
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Problem with MAS5 calls on MoEx array

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
>
>


The University of Glasgow, charity number SC004401