[BioC] Problem with MAS5 calls on MoEx array

Peter Saffrey pzs at dcs.gla.ac.uk
Mon Feb 8 19:23:14 CET 2010


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

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  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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