[BioC] trouble with cdf, .qcdef file

[Laurent Gatto]

Dear Kurt,

On Thu, Dec 10, 2009 at 8:41 PM, Marek, Kurt <kmarek at ucsd.edu> wrote:
> 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.


The alpha1 and alpha2 values are cut-offs used to define if a probe is
called present (p<alpha1), marginal (alpha1<p<alpha2) or absent
alpha2<p (where p is the p-value from the Wilcoxon Signed Rank test
used in MAS5). The default values are 0.04 and 0.06 for alpha1 and
alpha2 respectively.  In simpleaffy's qcdef files, alpha1 is 0.04 or
0.05 and alpha2 is 0.06 or 0.065. I don't know why/when these values
are modified, but I don't think that this would have any important
effect on the QC analysis.
Regarding the probe ids, the multiple entries are different probes
(sometime overlapping if I remember well) for the same target. As far
as I know, the results should be very similar, at least from a QC
point of view.
I don't know which degradation probes work best for your array. May be
there are some hints on Affymetrix's Netaffx page (free registration
required). If in doubt, you could still compare the results with
different probes.

Hope this helps,

Laurent

>
> 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
>>>
>>> _______________________________________________ Bioconductor mailing
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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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>
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