'ATH1121501.db'
Dear all,
Can anyone explain me why in the Arabidopsis annotation package
'ath1121501.db' there are no Entrez.Gene IDs, while in the other similar
they are present.
It creates me the problem as I need to realize an analysis of the results
from a microarray chip using GOstats, e.g. hypergeometric test. For this I
need to create a 'GOHyperGParams' object, which has as the argument the name
of the annotation package, from which it takes the data regarding
Entrez.Gene.Ids and correspondent GO annotation. Once Entrez is not present
it returns me the following error

Ошибка в getUniverseHelper(probes, datPkg, entrezIds) :
After filtering, there are no valid IDs that can be used as the Gene
universe.
Check input values to confirm they are the same type as the central ID used
by your annotation package.
For chip packages, this will still mean the central GENE identifier used by
the package (NOT the probe IDs).

for creating the 'universeGeneIds' I used Entrez Ids from the whole chip,
but I got them from NetAffx, because I couldnot from 'ath1121501.db' .

Also, I consulted the "Bioconductor Case Studies" book, where all the
examples are for 'hgu95av2.db', which contains the posibility to extract
ENTREZIDs.

Please, let me know anyone if I am wrong in something, or what can I do. If
there is another possibility to use an alternative of GOstats for the aim of
performing hypergeometric test.

Regards,
Alex from Moldova

-- 
Laboratorul Bioinformatica
Centrul Biologe Moleculara
Universitatea Academiei de Stiinte din Moldova

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