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

[James W. MacDonald]

Hi Kaj,

I don't see anything obviously wrong with your script.

I do wonder why you are bothering with loess normalization. Maybe 10 
years ago, normalization of Affy arrays was a relatively hot topic, but 
people have since pretty much settled on quantile normalization. I 
don't mean to imply that you should be using quantile normalization to 
normalize samples from three different experiments - that would be 
crazy - but I don't think you will be able to do a better job with 
cyclic loess. And none of the normalization routines are designed to 
account for batch effects, so you shouldn't really be normalizing all 
the arrays together anyway.

Instead, you might consider normalizing data from each experiment 
separately, and then using ComBat() from the sva package to remove the 
batch effects. Alternatively you could use SCAN.UPC to summarize your 
data.

Best,

Jim


On Sunday, January 26, 2014 11:42:01 PM, Kaj wrote:
> 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

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099