Question: problem with creating array annotation package
0
gravatar for Guido Hooiveld
6.3 years ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:
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 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.2 years ago by cstrato3.9k • written 6.3 years ago by Guido Hooiveld2.5k
Answer: problem with creating array annotation package
0
gravatar for Marc Carlson
6.2 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Guido, So Chinese Hamster is not supported with a schema etc. I actually have plans in the works to generalize things so that organisms that have not been supported in the past can start to be supported in this way, but 1st I have to make the code that generates the org packages more general and robust. You are correct that the problem is that internally the code is expecting a schema to be present in AnnotationDbi (and that knows based on a field in the metadata which schema to use). In your case, there is no schema and the metadata is pointing to the wrong schema as well (and thus also to the wrong org package). I have an idea for a way you might be able to hack this to make it partially functional. Send me a separate email if you are interested in trying this. Marc On 09/09/2013 12:48 PM, Hooiveld, Guido wrote: > 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 at wur.nl > internet: http://nutrigene.4t.com > http://scholar.google.com/citations?user=qFHaMnoAAAAJ > http://www.researcherid.com/rid/F-4912-2010 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.2 years ago by Marc Carlson7.2k
Answer: problem with creating array annotation package
0
gravatar for cstrato
6.2 years ago by
cstrato3.9k
Austria
cstrato3.9k wrote:
Dear Guido, In principle you could use package xps for the analysis of CHO arrays. It uses the clf/pgf-files and annotation files from Affymetrix. To create a 'scheme' file for xps you can for example do: library(xps) libdir <- "/Volumes/GigaDrive/Affy/libraryfiles" anndir <- "/Volumes/GigaDrive/Affy/Annotation" scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" # CHOGene-2_0-st: used as exon array scheme.chogene20st <- import.exon.scheme("chogene20st", filedir = file.path(scmdir, "na33"), file.path(libdir, "CHOGene-2_0-st.clf"), file.path(libdir, "CHOGene-2_0-st.pgf"), file.path(anndir, "Version13Mar", "CHOGene-2_0-st-v1.na33.2.crigri1.probeset.csv"), file.path(anndir, "Version13Mar", "CHOGene-2_0-st-v1.na33.2.crigri1.transcript.csv")) Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._
ADD COMMENTlink written 6.2 years ago by cstrato3.9k
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