[BioC] question of justRMA on exon array

[James W. MacDonald]

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

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

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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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099