Entering edit mode
Rhonda DeCook
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90
@rhonda-decook-1033
Last seen 10.2 years ago
Rich,
Can you tell us a little more. How was your custom CDF file created?
It seems
like R is not recognizing the file in your directory as a CDF file. I
created
a custom CDF file recently for the ATH1 chip that removed known 'SFP'
probe
pairs using the 'altcdfenv' package and a modification of functions in
the 'matchprobes' package (provided to me by Holger Schwender after I
posted
to this list). I eventually got everything running with the new CDF
file
assigned to my affybatch and I didn't have to go into the CEL files
and hand
edit the CDF file name on any of the 30 chips. I'll see if I can help
after
you send a little more info.
Rhonda
>
> I have created a custom CDF file.
>
> The purpose is to measure the expression of splice
> variations.
>
> I place the file in the same directory as the CEL
> files and crank up R and do the usual BIOC
> incantation.
>
> Based on a suggestion offered by the brainiacs at
> University of Michigan (
>
http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf
readme.htm
#How_to_use_the_custom_CDF_file:_
> )
> I try something like this ...
>
> data<-ReadAffy();
> data@cdfName<-"NEW.CDF"
>
> But subsequent data processing calls attempt to
> connect to the internet and get a CDF file from there.
>
> Obviously, I missing something.
>
> Anybody got any ideas?
>
> Please add to any "RTFM" responses a specific FM to
> read.
>
> Thanks!
>
> Rich
>
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