[BioC] Problem when trying to use \'affy\' package

Kaj Chokeshaiusaha [guest] guest at bioconductor.org
Sun Jan 19 14:45:36 CET 2014

Dear R helpers,

I have been learning 'affy' package and currently trying 'expresso' function of which allows background correction, normalization, PMcorrection and summarization in on step. I have try 'expresso' with following script with the "af" Affybatch

loess.none.mas <- expresso(af,normalize.method="loess",

#It continues computing till it gives an error as following 
Done with 5 vs 22 in iteration 1 
Done with 5 vs 23 in iteration 1 
Done with 5 vs 24 in iteration 1 
Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize,  : 
  NA/NaN/Inf in foreign function call (arg 1)

Could you please tell me what happens and how to correct it?

 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=Thai_Thailand.874  LC_CTYPE=Thai_Thailand.874   
[3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C                 
[5] LC_TIME=Thai_Thailand.874    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] affy_1.36.1        Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] affyio_1.26.0         BiocInstaller_1.8.3   preprocessCore_1.20.0
[4] zlibbioc_1.4.0  

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list