[BioC] trouble with cdf, .qcdef file
James W. MacDonald
jmacdon at med.umich.edu
Thu Dec 10 20:12:53 CET 2009
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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