[BioC] missing probeids in mu11ksuba metadata

[Dick Beyer]

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