[BioC] trouble with cdf, .qcdef file

[James W. MacDonald]

Hi Kurt,

Marek, Kurt wrote:
> I am trying to run affyQAReport on some X. tropicalis arrays. I keep
> getting the following error: Error in setQCEnvironment(cdfn) : Could
> not find array definition file ' xtropicaliscdf.qcdef '.
> 
> I downloaded the package xtropicaliscdf and loaded it in to the
> workspace, but that doesn't seem to help. The vignette refers to
> creating a .qcdef file, but I sort of thought this would be available
> somewhere. Is there a site that contains all of the .qcdef files? Is
> there a way to know which array types affyQAReport 'knows about'?

Sure.

 > library(simpleaffy)
 > dir(paste(.path.package("simpleaffy"), "extdata", sep = "/"))
  [1] "atgenomecdf.qcdef"
  [2] "ath1121501cdf.qcdef"
  [3] "celeganscdf.qcdef"
  [4] "drosgenome1cdf.qcdef"
  [5] "hcg110cdf.qcdef"
  [6] "hgfocuscdf.qcdef"
  [7] "hgu133a2cdf.qcdef"
  [8] "hgu133acdf.qcdef"
  [9] "hgu133atagcdf.qcdef"
[10] "hgu133bcdf.qcdef"
[11] "hgu133plus2cdf.qcdef"
[12] "hgu95acdf.qcdef"
[13] "hgu95av2cdf.qcdef"
[14] "hgu95bcdf.qcdef"
[15] "hgu95ccdf.qcdef"
[16] "hgu95dcdf.qcdef"
[17] "hgu95ecdf.qcdef"
[18] "mgu74acdf.qcdef"
[19] "mgu74av2cdf.qcdef"
[20] "mgu74bcdf.qcdef"
[21] "mgu74bv2cdf.qcdef"
[22] "mgu74ccdf.qcdef"
[23] "mgu74cv2cdf.qcdef"
[24] "moe430acdf.qcdef"
[25] "mouse4302cdf.qcdef"
[26] "mouse430a2cdf.qcdef"
[27] "mouse430b2cdf.qcdef"
[28] "mu11ksubacdf.qcdef"
[29] "mu11ksubbcdf.qcdef"
[30] "poplarcdf.qcdef"
[31] "porcinecdf.qcdef"
[32] "rae230acdf.qcdef"
[33] "rae230bcdf.qcdef"
[34] "rat2302cdf.qcdef"
[35] "rgu34acdf.qcdef"
[36] "rgu34bcdf.qcdef"
[37] "rgu34ccdf.qcdef"
[38] "rhesuscdf.qcdef"
[39] "soybeancdf.qcdef"
[40] "vitisviniferacdf.qcdef"
[41] "yeast2cdf.qcdef"
[42] "ygs98cdf.qcdef"
[43] "zebrafishcdf.qcdef"

So most of them are there. However, yours doesn't appear to be there, so 
you will have to follow the instructions in the vignette to create one.

Best,

Jim


> 
> thanks! Kurt
> 
> 
> Kurt Marek, Ph.D.
> 
> Division of Biological Sciences, Neurobiology Section University of
> California, San Diego 9500 Gilman Dr., Pacific Hall 3222B Mail Box
> 0357 La Jolla, CA 92093 Ph: 858-534-2456 kmarek at ucsd.edu
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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