[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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