[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
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
More information about the Bioconductor
mailing list