[BioC] simpleAffy with bovine cdf

[Paul Geeleher]

I might as well follow this up. I created the bovinecdf.qcdef file
myself. I'm fairly sure what is below is correct. It seems to work
anyway. Copy and paste the text below into bovinecdf.qcdef and save in
RHOME/library/simpleaffy/extdata. Eg.
/usr/local/lib/R/library/simpleaffy/extdata/bovinecdf.qcdef


array bovinecdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-BioB-3_at
spk bioC AFFX-BioC-3_at
spk bioD AFFX-BioDn-3_at
spk creX AFFX-CreX-3_at
ratio actin3/actin5 AFFX-Bt-actin-3_at AFFX-Bt-actin-5_at
ratio actin3/actinM AFFX-Bt-actin-3_at AFFX-Bt-actin-M_at
ratio gapdh3/gapdh5 AFFX-Bt-gapd-3_at AFFX-Bt-gapd-5_at
ratio gapdh3/gapdhM AFFX-Bt-gapd-3_at AFFX-Bt-gapd-M_at


On 4/15/08, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> Hi,
>
> When I try to run a simpleAffy plot on my data, using a bovine CDF, I
> get an error saying:
>
> "Could not find array definition file 'bovinecdf.qcdef'."
>
> I wonder if this file is available anywhere? Or will I have to create it
> myself?
>
> I'm also wondering if a similar file might be available for the
> affyprobeminer custom CDF files?
>
> Thanks for any help,
>
> -Paul.
>