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

[James W. MacDonald]

Hi Kaj,

On Sunday, January 19, 2014 8:45:36 AM, Kaj Chokeshaiusaha [guest] 
wrote:
>
> 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",
>              bgcorrect.method="none",
>              pmcorrect.method="mas",
>              summary.method="mas")
>
> #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?

You will need to give us more information than that. How did you 
generate the AffyBatch you are using? What array? What exactly are you 
trying to do?

Best,

Jim


>
>
>   -- output of sessionInfo():
>
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [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.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099