Thank you very much, James!!

I will try my best to figure this out. It's always great for naive person
like me to have generous person like you in Bioconductors :)

Best Regards,
Kaj


On Thu, Jan 30, 2014 at 9:31 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Kaj,
>
> If you are really interested in figuring out what the problem is, then it
> will be up to you. As I already told you, I don't see anything obvious with
> your script.
>
> Anyway, the error you see comes from stats:::simpleLoess(), which can't
> have any NA values. However, this function is called by stats::loess, which
> _can_ have NA values:
>
>  y <- rnorm(1000)
>> x <- rnorm(1000)
>> y[sample(1:1000, 50)] <- NA
>> loess(y~x)
>>
> Call:
> loess(formula = y ~ x)
>
> Number of Observations: 950
> Equivalent Number of Parameters: 5.49
> Residual Standard Error: 1.061
>
> But if we use stats:::simpleLoess() directly:
>
>  stats:::simpleLoess(y,x,rep(1, 1000))
>>
> Error in stats:::simpleLoess(y, x, rep(1, 1000)) :
>
>  NA/NaN/Inf in foreign function call (arg 1)
>
> The reason loess() has no problems with the NA values is because it looks
> at
>
>  options("na.action")
>>
> $na.action
> [1] "na.omit"
>
> and omits the paired observations where one or the other is NA. I don't
> see that normalize.loess() cares much about NA values, however:
>
>  z <- normalize.loess(cbind(x,y))
>>
> Done with 1 vs 2 in iteration 1
> 1 NA
> Warning message:
> In normalize.loess(cbind(x, y)) : NaNs produced
>
> although the normalized values are really bad:
>
>  apply(z, 2, function(x) sum(is.na(x)))
>>
>  x   y
> 766 766
>
> So I guess the first step is to run your script and then see what you get
> for options("na.action"). If that is not na.omit then you have a problem.
> But if you have any NA values in your AffyBatch, you still have a problem
> because you shouldn't have any. If no NA values, then you will probably
> have to either debug(loess) and step through, checking for NA values being
> passed in and then go back and try to find out why, or use options(error =
> recover) and then inspect the various frames that come up when you hit the
> error.
>
> Best,
>
> Jim
>
>
>
>
> On Wednesday, January 29, 2014 9:50:36 PM, Kaj wrote:
>
>> 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.
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor@r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>
>>>>> --
>>>>> 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
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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