[BioC] building annotation package for porcine

Javier Pérez Florido jpflorido at gmail.com
Wed Mar 24 23:38:13 CET 2010


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



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