[BioC] missing probeids in mu11ksuba metadata

[Ting-Yuan Liu]

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
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