[BioC] trouble with cdf, .qcdef file

[Marek, Kurt]

James,
Thanks for your response. I'm trying to generate my own file based on the vignette, but I'm not exactly sure what values to enter. alpha1 and alpha2 are complete mysteries to me; where do I find these? I know the others are probe IDs, but there are multiple entries for all of them in the array annotation file. For instance, there is AFFX-BioB-3_at and AFFX-r2-Ec-bioB-3_at. I went with the latter since it most closely resembles the example in the vignette, but I'm not sure what the difference is. For the ratios, I am using AFFX-Str-actin-3_at and AFFX-Str-actin-5_at, but there is also a AFFX-Str-actin-3_x_at. Any additional explanation of these values or where I might find some additional explanation would be most appreciated.

Thanks!
Kurt


On Dec 10, 2009, at 11:12 AM, James W. MacDonald wrote:

> 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
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