[Bioc-devel] yeast2 metadata

[John Zhang]

>The probe number missmatch may because of these codes in function
>getProbe2SGD.:
>
>    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
>ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/orf_g
eneontology.tab. 
>
>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. 


>thanks
>
>nianhua
>
>> I would ask if it would be possible not to release metadata packages showing 
>> missmatches.
>>
>> regards and thanks for any comment
>>
>> mattia
>>
>>
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084