[BioC] missing probeids in mu11ksuba metadata

[Dick Beyer]

Ting, Thanks very much, Dick

*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Tue, 21 Feb 2006, Ting-Yuan Liu wrote:

>
> Hi Dick,
>
> This situation is resulted from the inconsistence of Affymetrix Mu11KsubA
> CDF file.  In this file, I found that Affymetrix confused
> "AF027865_1_s_at" and "AF027865_s_at" in "Unit3403_Block1", and Affymetrix
> also confused "AF027865_2_s_at" and "af027865_s_at" in "Unit3404_Block1".
>
> I believe that "AF027865_1_s_at" and "AF027865_2_s_at" should replace
> "AF027865_s_at" and "af027865_s_at", respectively, according to the
> annotation file Affymetrix provides.
>
> I will report this bug to Affymetrix and hopefully they will correct this
> soon.
>
> Thanks for this report.
>
> Sincerely,
> Ting
> ______________________________________
> Ting-Yuan Liu
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> Seattle, WA, USA
> ______________________________________
>
> On Mon, 20 Feb 2006, Dick Beyer wrote:
>
>> I have found one or more affy probeids in Mu11KsubA are missing. A query at the netaffx site shows, for Mu11KsubA, there are these two probes:
>>
>> AF027865_1_s_at
>> AF027865_2_s_at
>>
>> In my R session, I have
>>
>>> tmp
>> AffyBatch object
>> size of arrays=534x534 features (2232 kb)
>> cdf=Mu11KsubA (6584 affyids)
>> number of samples=1
>> number of genes=6584
>> annotation=mu11ksuba
>>
>>> grep("AF027865_1_s_at",geneNames(tmp),ignore.case=TRUE)
>> numeric(0)
>>
>> z <- grep("AF027865",geneNames(tmp),ignore.case=TRUE)
>>> geneNames(tmp)[z]
>> [1] "af027865_s_at" "AF027865_s_at"
>>
>> So the mu11ksuba metadata is missing the probeids and in their place are two identical probeids.
>>
>> Is this an error in the mu11ksuba metadata, or are probes that have "_1_" and "_2_" variants in the original platform handled with upper and lower case leading letters?
>>
>> Thanks much,
>> Dick
>> *******************************************************************************
>> Richard P. Beyer, Ph.D.	University of Washington
>> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
>>  			Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>> http://staff.washington.edu/~dbeyer
>>
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>