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

[Kaj]

On 28/01/14 00:22, James W. MacDonald wrote:
> 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
Dear Jim,

To tell you the truth, I already try other normalization methods 
combined with batch correction using ComBat. I'm trying to determine 
which methods are the best to pre-process the data.

There should be something wrong with my script trying Cyclic Loess. 
Could you please guide me a bit?

Best Regards,
Kaj