[Bioc-devel] yeast2 metadata

Mattia Pelizzola mattia.pelizzola at unimib.it
Thu Jul 20 14:36:06 CEST 2006

Dear all, 

I wonder why some very important environments are missing in the yeast2 
annotation package (in both 1.8 and 1.7 bioC releases). For instance the 
ACCNUM and the SYMBOL environments are missing, while the GENENAME env is 
available. This would be a problem in writing scripts that can be applied to 
a generic Affy annotation package.

Moreover, in both 1.8 and 1.7 bioC releases, the yeast2 package has some 
problems in the quality checks. For example for the old one:

Quality control information for  yeast2
Date built: Created: Tue Oct  4 19:23:39 2005

Number of probes: 10928
Probe number missmatch: yeast2ALIAS; yeast2CHRLOC; yeast2CHR; 
yeast2DESCRIPTION; yeast2ENZYME; yeast2GENENAME; yeast2GO; yeast2ORF; 
yeast2PATH; yeast2PMID
Probe missmatch: None
Mappings found for probe based rda files:
         yeast2ALIAS found 1759 of 10928
         yeast2CHRLOC found 4962 of 10928
         yeast2CHR found 5645 of 10928
         yeast2DESCRIPTION found 5631 of 10928
         yeast2ENZYME found 778 of 10928
         yeast2GENENAME found 4335 of 10928
         yeast2GO found 5645 of 10928
         yeast2ORF found 6356 of 10928
         yeast2PATH found 1110 of 10928
         yeast2PMID found 5454 of 10928
Mappings found for non-probe based rda files:
         yeast2CHRLENGTHS found 17
         yeast2ENZYME2PROBE found 446
         yeast2GO2ALLPROBES found 3870
         yeast2GO2PROBE found 2615
         yeast2ORGANISM found 1
         yeast2PATH2PROBE found 99
         yeast2PMID2PROBE found 34881

I previously experienced problems regarding the "Probe number missmatch", but 
usually the total number of probes was less than the number of probes in the 
corresponding cdf package, and the annotation was very poor. In this case the 
number of probesets seems to be ok, while I'm not able to evaluate the amount 
of annotated probesets.

I would ask if it would be possible not to release metadata packages showing 

regards and thanks for any comment


Mattia Pelizzola
PhD Student
Genopolis Consortium
Milano-Bicocca University
P.zza della Scienza 4
20126 Milano (Italy)

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