Hello,

R version: 2.8.0

I just installed the hgu133plus2.db package, and am looking at the hgu133plus2CHRLOC environment. I've noticed that some of the probeset entries (e.g. "201268_at") have multiple locations compared to Affy's annotation file. I'd like to figure out if these multiple locations are current, in which case it is some sort of overlapping/repeating duplication. For example:

> as.list(hgu133plus2CHRLOC)$'201268_at'
      17       17       17       17 
46598879 46597889 46598637 46599081 

indicates that the probeset maps to 4 locations. Compare this to the alignments info in the Affy's annotation file (from 7/8/08, http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/HG-U133_Plus_2.na26.annot.csv.zip): 

chr12:119204403-119205041 (+) // 91.49 // q24.31 /// chr17:46598810-46604103 (+) // 96.87 // q21.33

which suggests one location on chromosome 17 (I'm ignoring chromosome 12 for now). This is a "_at" probeset, so it should map uniquely to a sequence, according to Affy's "Data Analysis Fundamentals" document (and speaking to a rep).

From the information provided by "?hgu133plus2CHRLOC", I downloaded 
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/affyU133Plus2.txt.gz 
from UCSC to see how this occured, but it is not clear. Actually, the file:
http://www.affymetrix.com/Auth/analysis/downloads/psl/HG-U133_Plus_2.link.psl.zip
from Affy's support page has the same alignment info. Here's the relevant PSL info:

Target sequence name: chr17
Alignment start position in target: 46598810
Alignment end position in target: 46604103
Number of blocks in the alignment (a block contains no gaps): 5
Comma-separated list of sizes of each block: 47,130,102,113,257,
Comma-separated list of starting positions of each block in target: 46598810,46599186,46600601,46602296,46603846,


The second location provided by CHRLOC (46597889) occurs before the start of the alignment in the PSL info, so perhaps this one CHRLOC location corresponds to the PSL alignment? The mappings were obtained from UCSC on 2006-Apr14, so perhaps additional alignments existed at the time, which have since been removed.


Thank you for any help. Hopefully I'm just missing something obvious (well, non-obvious for me).

Peter Bazeley

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