Hi Kurt,
Marek, Kurt 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.
I don't know how much help I can be, as I have essentially no
experience
with this package. The only suggestion I would have is to look at the
values in the other .qcdef files (particularly those that you think
are
'closer' to X. tropicalis by some measure) and see if there is some
sort
of consensus.
You could also search the mailing list. I usually go here:
http://dir.gmane.org/gmane.science.biology.informatics.conductor
and then type in some nonsense like sllsfjd, which will get you here:
http://search.gmane.org/?query=sllsfjd&group=gmane.science.biology.inf
ormatics.conductor
You can then search for reasonable terms and add 'miller' in the
'written by' field so you just get responses from the main man
himself.
Best,
Jim
>
> 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
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>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
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>>>
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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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and
>> should not be used for urgent or sensitive issues
>>
>
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues
