simpleAffy with bovine cdf
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Paul Geeleher ★ 1.3k
@paul-geeleher-2679
Last seen 7.2 years ago
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.
cdf simpleaffy cdf simpleaffy • 516 views
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Entering edit mode
Paul Geeleher ★ 1.3k
@paul-geeleher-2679
Last seen 7.2 years ago
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. >
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