Hi James,

Thanks for your reply. No, I did not get that idea from anywhere, I am a
newbie to Exon array, although I have analyzed a lot of Gene 1.0 ST array.
I thought Exon array should be very similar to Gene ST array, that's why I
thought justRMA should work for them (since justRMA works fine for Gene ST
array).

I'll give a shot on what you proposed to see how it works.

Thanks again,

-Jack

On Mon, Jan 14, 2013 at 5:20 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Jack,
>
>
> On 1/14/2013 4:30 PM, Jack Luo wrote:
>
>> Hi,
>>
>> I am trying to RMA normalize a bunch of exon arrays. I thought this is as
>> easy as what I have done with the gene 1.0 ST array by using justRMA.
>> However, it has the error information:
>>
>> *.CEL does not seem to have cdf information
>>
>> I provided the path of the CDF I downloaded from Affy website, but it does
>> not help.
>>
>
> Where did you get the idea that would work? Note that I am not trying to
> be critical, I am really interested in knowing.
>
> Anyway, that's not how things work. You can't just point to an Affy CDF
> and have things work out, you have to install a cdf package that was built
> for R. Normally this is an automagic install, but in this case there isn't
> a pre-built cdf.
>
> I don't recall why I have never built a cdf package for this array, but I
> just tried and it segfaults, so that is likely why. Well, that and the fact
> that the affy package was never intended to be used with these arrays so I
> have a pre-existing antipathy towards doing this. But if you insist, you
> can get alternate versions here:
>
> http://dmp.i-med.ac.at/index.**php/en/resources/bioinfo-menu-**
> custom-cdf-jumi<http://dmp.i-med.ac.at/index.php/en/resources/bioinfo-menu-custom-cdf-jumi>
>
> Download the CDF R Package, and then install using
>
> install.packages("**huex10stv268cdf_0.2.0.tar.gz", type="source", repos =
> NULL)
>
> or you can just add
>
> cdfname = "huex10stv2hsentrezgcdf"
>
> to your call to justRMA() to get the MBNI remapped version. You can get
> CDFs mapped based on any number of annotations, see for instance the
> Version 16 arrays here:
>
> http://brainarray.mbni.med.**umich.edu/Brainarray/Database/**
> CustomCDF/CDF_download.asp<http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp>
>
> Or you could do what IMO you should be doing anyway, and install oligo or
> xps and process with software that is intended for these arrays.
>
> Best,
>
> Jim
>
>
>
>> Any clues?
>>
>> Thanks a lot,
>>
>> -Jack
>>
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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
>
>

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