[BioC] missing probeids in mu11ksuba metadata
Ting-Yuan Liu
tliu at fhcrc.org
Tue Feb 21 19:17:02 CET 2006
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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