[BioC] want to compare hgu133a and hgu133plus2

Dick Beyer dbeyer at u.washington.edu
Tue Sep 27 16:52:07 CEST 2005

I have a data set with a mix of hgu133a and hgu133plus2.  I was wondering if anyone has a simple or straightforward way of finding the common probesets between the chips.

What I have found are two sources, TIGR resourcerer and Affy, that have several choices.

>From resourcerer I get:
affy_U133a & affy_U133Plus2 based on EGO 27005 entries
affy_U133a & affy_U133Plus2 based on UniGene 61545 entries
affy_U133a & affy_U133Plus2 based on RefSeq 15705 entries

>From Affy I get:
hgu133_vs_hgu133_plus_complex.txt 3367535 entries
hgu133_vs_hgu133_plus_best.txt 107 entries
hgu133_vs_hgu133_plus_good.txt 110 entries
hgu133_vs_hgu133_plus_none.txt 9 entires

For most of these files, there are many U133plus2 probesets for each U133a probeset.

I am hoping someone has figured out a script to extract the optimum one-to-one mapping (if that is even a good approach) from one of these sources, or would point me to information about how best to do compare the data from the two different chips.

Thanks very much for any help,
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

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