Dear Marc, I tried to run your suggested code to generate a porcine annotation package in 2.12.0 (64-bit). However it returns a cryptic error message. Any help would be most appreciated. (The csv file was downloaded from NetAffx today.) Cheers, Fraser > library(AnnotationDbi) > makeDBPackage("PIGCHIP_DB", + affy=TRUE, + prefix="Porcine", + fileName="Porcine.na31.annot.csv", + baseMapType="gbNRef", + outputDir = ".", + version="1.0.0", + manufacturer = "Affymetrix", + chipName = "Porcine", + manufacturerUrl = "http://www.affymetrix.com") Error in `[.data.frame`(csvFile, , GenBankIDName) : undefined columns selected > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationDbi_1.12.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 RSQLite_0.9-2 > -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc Carlson Sent: Wednesday, March 24, 2010 7:10 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] building annotation package for porcine Hi Javier, You are VERY close. The main trouble is that your schema is the wrong kind. You want to use a chip schema (PIGCHIP_DB) because you are making a chip package. The other kind of schema (PIG_DB, HUMAN_DB etc.) is reserved for making org packages, and we already make those for you. Here is what I used (note that the outputDir is for unix): makeDBPackage("PIGCHIP_DB", affy=TRUE, prefix="Porcine", fileName="Porcine.na30.annot.csv", baseMapType="gbNRef", version="1.0.0", manufacturer = "Affymetrix", chipName = "Porcine", manufacturerUrl = "http://www.affymetrix.com") This should create a source directory for you called Porcine.db Once you have the source directory, you should be able to build, check and install it as with any other source package for R. Marc On 03/24/2010 03:38 PM, Javier P?rez Florido wrote: > Dear list, > I am using an affymetrix porcine data set and, before differential > expression using limma, I would like to use non-specific filtering > using nsFilter function from genefilter package. > I understood that there is no annotation package for porcine arrays > (unless I am wrong), so, one choice is to build an annotation package > to be used in the nsFilter function from the original Affymetrix > annotation file. > > For this purpose, I think I can use the makeDBPackage function from > AnnotationDbi package, but I am not able to manage it. I've tried with > the following chunk of code: > > library(pig.db0) > > makeDBPackage("PIG_DB", > affy=TRUE, > prefix="Porcine", > fileName="Porcine.na30.annot.csv", > baseMapType="gb", > outputDir = "C:/", > version="1.0.0", > manufacturer = "Affymetrix", > chipName = "Porcine", > manufacturerUrl = "http://www.affymetrix.com") > > The csv file is the one related to porcine annotation downloaded from > Affymetrix and it is in the same working directory. The result of > executing this code is NULL. I've tried also with the following code > > makeDBPackage("HUMANCHIP_DB", > affy=FALSE, > prefix="hcg110", > fileName=hcg110_IDs, > baseMapType="gb", > outputDir = tmpout, > version="1.0.0", > manufacturer = "Affymetrix", > chipName = "Human Cancer G110 Array", > manufacturerUrl = "http://www.affymetrix.com") > > and it works, so, clearly, it is something wrong in my code that I'm > not able to see... > > Any suggestions? > Thanks in advance, > Javier > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Fraser, The problem appears to be that Affymetrix has started to add header lines to the top of their .csv files. My code wasn't expecting that which is why you got that error. I will fix this, and also add a pre-made porcine.db package to the repository for you. But in the meantime you can make your code work by removing the lines that start with a # from the top of the "Porcine.na31.annot.csv" file. Marc On 11/01/2010 03:03 PM, Fraser Sim wrote: > Dear Marc, > > I tried to run your suggested code to generate a porcine annotation package > in 2.12.0 (64-bit). However it returns a cryptic error message. Any help > would be most appreciated. (The csv file was downloaded from NetAffx today.) > > Cheers, > Fraser > > >> library(AnnotationDbi) >> makeDBPackage("PIGCHIP_DB", >> > + affy=TRUE, > + prefix="Porcine", > + fileName="Porcine.na31.annot.csv", > + baseMapType="gbNRef", > + outputDir = ".", > + version="1.0.0", > + manufacturer = "Affymetrix", > + chipName = "Porcine", > + manufacturerUrl = "http://www.affymetrix.com") > Error in `[.data.frame`(csvFile, , GenBankIDName) : > undefined columns selected > >> sessionInfo() >> > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AnnotationDbi_1.12.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 RSQLite_0.9-2 > >> > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc Carlson > Sent: Wednesday, March 24, 2010 7:10 PM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] building annotation package for porcine > > Hi Javier, > > You are VERY close. The main trouble is that your schema is the wrong > kind. You want to use a chip schema (PIGCHIP_DB) because you are making > a chip package. The other kind of schema (PIG_DB, HUMAN_DB etc.) is > reserved for making org packages, and we already make those for you. > > Here is what I used (note that the outputDir is for unix): > > > makeDBPackage("PIGCHIP_DB", > affy=TRUE, > prefix="Porcine", > fileName="Porcine.na30.annot.csv", > baseMapType="gbNRef", > version="1.0.0", > manufacturer = "Affymetrix", > chipName = "Porcine", > manufacturerUrl = "http://www.affymetrix.com") > > This should create a source directory for you called Porcine.db Once > you have the source directory, you should be able to build, check and > install it as with any other source package for R. > > > Marc > > > > On 03/24/2010 03:38 PM, Javier P?rez Florido wrote: > >> Dear list, >> I am using an affymetrix porcine data set and, before differential >> expression using limma, I would like to use non-specific filtering >> using nsFilter function from genefilter package. >> I understood that there is no annotation package for porcine arrays >> (unless I am wrong), so, one choice is to build an annotation package >> to be used in the nsFilter function from the original Affymetrix >> annotation file. >> >> For this purpose, I think I can use the makeDBPackage function from >> AnnotationDbi package, but I am not able to manage it. I've tried with >> the following chunk of code: >> >> library(pig.db0) >> >> makeDBPackage("PIG_DB", >> affy=TRUE, >> prefix="Porcine", >> fileName="Porcine.na30.annot.csv", >> baseMapType="gb", >> outputDir = "C:/", >> version="1.0.0", >> manufacturer = "Affymetrix", >> chipName = "Porcine", >> manufacturerUrl = "http://www.affymetrix.com") >> >> The csv file is the one related to porcine annotation downloaded from >> Affymetrix and it is in the same working directory. The result of >> executing this code is NULL. I've tried also with the following code >> >> makeDBPackage("HUMANCHIP_DB", >> affy=FALSE, >> prefix="hcg110", >> fileName=hcg110_IDs, >> baseMapType="gb", >> outputDir = tmpout, >> version="1.0.0", >> manufacturer = "Affymetrix", >> chipName = "Human Cancer G110 Array", >> manufacturerUrl = "http://www.affymetrix.com") >> >> and it works, so, clearly, it is something wrong in my code that I'm >> not able to see... >> >> Any suggestions? >> Thanks in advance, >> Javier >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >