Hi Marc and others,
I would like to create an annotation package for an microarray, but I am stuck. Could you please advise how to do this?
- We are analyzing CHO samples on a Chinese Hamster microarray.
- I have mapped the probesets on the array to corresponding RefSeq IDs.
- As you may recall, I have created a org.db (org.Cgriseus.eg.db) using the function makeOrgPackageFromNCBI()
- I am following the vignette / PDF "SQLForge: An easy way to create a new annotation package with a standard database schema."

Problem I face now is which database scheme to use.
For the well-studied organisms like human, mouse, pig, etc a scheme is available, but for Chinese Hamster that is not the case.
As test I just used the "MOUSECHIP_DB" database scheme, but this seems not to work; see error below. I *think* this is because under the hood the mouse org.db is accessed, which obviously doesn't have annotation info for Chinese Hamster RefSeq IDs... If so, how then to point to the 'org.Cgriseus.eg.db'?

Any pointers are appreciated!
Thanks,
Guido

> head(array.mapping)
                 V1           V2
1 NM_001243976.1_at NM_001243976
2 NM_001243977.1_at NM_001243977
3 NM_001243978.1_at NM_001243978
4 NM_001243979.1_at NM_001243979
5 NM_001243980.1_at NM_001243980
6 NM_001243981.1_at NM_001243981
>

> makeDBPackage("MOUSECHIP_DB",
+               affy=FALSE,
+               prefix="CH_Test",
+               fileName="D:\\CH\\array_mapping.txt",
+               baseMapType="refseq",
+               version="1.0.0",
+               manufacturer = "Affymetrix",
+               chipName = "Chinese Hamster Array",
+               manufacturerUrl = "http://www.affymetrix.com")
baseMapType is refseq
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: no such table: src.refseq)
>

---------------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email:      guido.hooiveld@wur.nl
internet:   http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010


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