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

[Kaj]

On 22/01/14 01:24, James W. MacDonald wrote:
> 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
Dear James,

I'm tremendously sorry for my late response.

Thank you very much for your attention and reply. Here attached the 
script I have tried lately. What I want to do is to pre-process CEL 
files of canine affymetrix platform acquired from different experiments.

Thank you very much again for your help.

Best Regards,
Kaj
-------------- next part --------------
##----------------------------------------------------------------------------
## Change stack limitation ##
##----------------------------------------------------------------------------
ulimit -s 32768
R --slave -e 'Cstack_info()["size"]'


##----------------------------------------------------------------------------
## R
##----------------------------------------------------------------------------

R
library(ArrayExpress)
require(arrayQualityMetrics)
require(affy)
require(Biobase)

##----------------------------------------------------------------------------
## Download raw data
##----------------------------------------------------------------------------
{
getAE("E-GEOD-25586", type="raw")
getAE("E-GEOD-22516", type="raw")
getAE("E-GEOD-20718", type="raw")
#After that I extract the zip files to acquire all CEL files
}

##---------------------------------------------------------------------------
## Outliner Detection for individual dataset - You can skip these steps
##---------------------------------------------------------------------------
{
E20718 <- as.vector(list.files(pattern = c("^GSM520","*.CEL")))
E22516 <- as.vector(list.files(pattern = c("^GSM559","*.CEL")))
E25586 <- as.vector(list.files(pattern = c("^GSM629","*.CEL")))

E20718 <- ReadAffy(filenames=E20718)
E22516 <- ReadAffy(filenames=E22516)
E25586 <- ReadAffy(filenames=E25586)

#I use arrayQualityMetrics here
arrayQualityMetrics(E20718)
arrayQualityMetrics(E22516)
arrayQualityMetrics(E25586)
##---------------------------------------------------------------------------
## 
##These are CEL files I decided to exclude from the overall datasets
bad <- c("GSM520205.CEL", "GSM520207.CEL", "GSM520216.CEL",
	 "GSM559083.CEL", "GSM559094.CEL",
	 "GSM629054.CEL")
microfiles <- as.vector(list.files(pattern = c("^GSM","*.CEL")))
remove = which(microfiles%in%bad)
microfiles = microfiles[-remove]
af <- ReadAffy(filenames=microfiles)
}
##---------------------------------------------------------------------------
## Trying cyclic loess using "expresso" function
##---------------------------------------------------------------------------
##Cyclicloess
{
loess.no_bg.mas5_correct.tb_sum <- expresso(af,normalize.method="loess",
		    bgcorrect.method="none",
		    pmcorrect.method="mas",
		    summary.method="mas")

loess.no_bg.pm_correct.tb_sum <- expresso(af,normalize.method="loess",
		    bgcorrect.method="none",
		    pmcorrect.method="pmonly",
		    summary.method="mas")

loess.no_bg.mas5_correct.med_sum <- expresso(af,normalize.method="loess",
		    bgcorrect.method="none",
		    pmcorrect.method="mas",
		    summary.method="medianpolish")

loess.no_bg.pm_correct.med_sum <- expresso(af,normalize.method="loess",
		    bgcorrect.method="none",
		    pmcorrect.method="pmonly",
		    summary.method="medianpolish")
}