[BioC] Problem with MAS5 calls on MoEx array

[cstrato]

Dear Peter,

The problem turned out to be a missing "#include <cstdlib>" in some 
source files, which gcc-4.3.2 did accept, while gcc-4.4.1 is more 
restrictive. Thus I have uploaded a new version "xps-1.6.3" to BioC, 
which should solve the problem.

Since I do not have gcc-4.4.1 and thus cannot test if the new version 
works, I would appreciate if you could test if xps-1.6.3 works on your 
system.

Best regards
Christian


Peter Saffrey wrote:
> 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
>>
>> _______________________________________________
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>>
>>
>>     
>
>
> The University of Glasgow, charity number SC004401
>
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