On 1/14/2013 4:30 PM, Jack Luo wrote:
> I am trying to RMA normalize a bunch of exon arrays. I thought this
> easy as what I have done with the gene 1.0 ST array by using
> 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
> not help.
Where did you get the idea that would work? Note that I am not trying
be critical, I am really interested in knowing.
Anyway, that's not how things work. You can't just point to an Affy
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,
I just tried and it segfaults, so that is likely why. Well, that and
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
insist, you can get alternate versions here:
Download the CDF R Package, and then install using
install.packages("huex10stv268cdf_0.2.0.tar.gz", type="source", repos
or you can just add
cdfname = "huex10stv2hsentrezgcdf"
to your call to justRMA() to get the MBNI remapped version. You can
CDFs mapped based on any number of annotations, see for instance the
Version 16 arrays here:
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.
> Any clues?
> Thanks a lot,
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099