[BioC] {Spam?} Re: RMA on a batch with NA values

[Kasper Daniel Hansen]

On Aug 11, 2008, at 9:50 AM, Tarca, Adi wrote:

> Thanks Jim,
>
> It looks like rma has an argument "subset" that allows me to choose  
> the
> probesets that I want to consider.
> Even discarding some probes out of the considered probesets can work  
> as
> well if no background correction is required, i.e.
>
> esetb<-rma(abatch,subset=psok, background=FALSE)
>
> works fine after inserting Nas.
>
> I just find strange that the background correction step requires that
> all probe intensities should be valid number and not contain any Nas.

Why? You will never have NA's in CEL files.

Kasper


> Regards,
> Adi
>
>
>
> Adi Laurentiu TARCA, Ph.D.
> Research Associate, Dept. of Computer Science &
> Services in Support of the NIH Perinatology Research Branch,
> Manager of the Bioinformatics Core, Karmanos Cancer Institute,
> Wayne State University,
> 3990 John R., Office 4809,
> Detroit, Michigan 48201
> Tel: 1-313-5775305
> Cell: 1-313-4043116
> http://vortex.cs.wayne.edu/tarca/
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: Monday, August 11, 2008 9:05 AM
> To: Tarca, Adi
> Cc: bioconductor at stat.math.ethz.ch
> Subject: {Spam?} Re: [BioC] RMA on a batch with NA values
>
> Hi Adi,
>
> Tarca, Adi wrote:
>> Hi all,
>> I am trying to run RMA using only a limited number of probes. I have
>> the x and y coordinates of those probes that I want to use.
>> The approach I have tried was to replace with NA all probe  
>> intensities
>
>> that I want to discard, but the RGUI gives an error and tries to end
>> the session. The console is still running but it does not return any
>> results.
>> Here is the code I use:
>>
>> #####
>> abatch<-ReadAffy(filenames=fnss,celfile.path="./CELL")
>> indok<-xy2indices(x=okx,y=oky,abatch=abatch)
>> ints<-intensity(abatch)
>> ints[-indok,]<-NA
>> intensity(abatch)<-ints
>> esetb<-rma(abatch)
>>
>> Any ideas?
>
> You won't be able to just set things equal to NA in order to remove  
> them
> from consideration.
>
> There is some code that Ariel Chernomoretz posted back in '05 that  
> might
> still work to remove particular probes from a probeset:
>
> http://article.gmane.org/gmane.science.biology.informatics.conductor/425
> 8/match=,
>
> Best,
>
> Jim
>
>
>>
>> Thanks,
>> Adi L. Tarca
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
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>
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