[BioC] What to do about the missing probe sequences for HG_U95A?

Thon de Boer thondeboer at yahoo.com
Wed Oct 6 06:13:24 CEST 2004


We are trying to develop a GC-RMA normalization plugin
for GeneSpring, but we are running into a problem with
missing probe sequence information for the HG_U95 chip

The probe_tab files that Affy is providing is missing
the probe sequences for 172 probesets, since
apparently, those sequences are only provided by TIGR
and Affy never got the OK to redistribute those probe
sequences...For the GC-RMA implementation, those probe
sequences are required to correctly calculate the
affinities for the probes and I was wondering if
anyone has the probe sequences for those missing

I looked at the probe sequences from the BioConductor
site, but those also seem to be missing some of these

Has anyone collected those probe sequences for those
172 missing probes, or do I have to go to the TIGR
site and retrieve them from there?


Thon de Boer
Silicon Genetics

More information about the Bioconductor mailing list