[Bioc-devel] yeast2 metadata

John Zhang jzhang at jimmy.harvard.edu
Fri Jul 21 19:57:20 CEST 2006

>The probe number missmatch may because of these codes in function
>    merged <- merge(probes, temp, by = by, all.x = TRUE)
>    merged <- merged[!duplicated(merged[, 1]), ]
>Here "probes" is the probeset ID to ORF ID mapping obtained from
>Affymetrix. All probeset IDs are included (10928 probeset IDs in total).
>"temp" is the ORF ID to SGD ID mapping obtained from
>They are first merged together, so still have 10928 probeset IDs. And
>then when multiple probeset IDs are mapped to the same ORF ID, only the
>first probeset ID is kept. Because the 10928 probeset IDs are mapped to
>only 6356 unique ORF IDs, only 6356 probeset IDs are kept for further
>annotation process. I guess that's why we get probe number mismatch. It
>seems this is the author's intention to remove probeset IDs with
>duplicated mappings. Maybe the author can explain more.

Probe number mismatch is not a serious problem but should be avoided. I will try 
to look at this when I get the chance. 

>> I would ask if it would be possible not to release metadata packages showing 
>> missmatches.
>> regards and thanks for any comment
>> mattia
>Bioc-devel at stat.math.ethz.ch mailing list

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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