[BioC] affymetrix pig annotation data

[Henrik Hornshøj Jensen]

I finally managed to put something together that works.

My basefile contains pig probe IDs mapped to human accession IDs using blast:

100049	NM_005384.2
100053	NM_214393.1
100055	NM_006219.1
100057	NM_016593.3

The code is below.

Henrik

#########################################
library(AnnBuilder)

myPkgName <- "PigArray"
myBase <- "mybasefile.txt"
myBaseRead <- read.table(myBase, sep = "\t", header = FALSE, as.is = TRUE)
myBaseType <- "gbNRef"
mySrcUrls <- getSrcUrl("all", "Homo sapiens")
myDir <- "C:/PigArray"

ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType,
pkgName = myPkgName, pkgPath = myDir,
organism = "Homo sapiens", version = "2.0.0",
author = list(author = "Henrik Hornshoj <henrikh.jensen at agrsci.dk>",
maintainer = "Henrik Hornshoj <henrikh.jensen at agrsci.dk>"),
fromWeb = TRUE)



-----Oprindelig meddelelse-----
Fra: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] På vegne af Henrik Hornshøj Jensen
Sendt: Tuesday, January 03, 2006 10:46 AM
Til: bioconductor at stat.math.ethz.ch
Emne: [BioC] affymetrix pig annotation data

Dear Morten Mattingsdal 
 
Sorry to bother you with this, but I just wondered if you ever managed to solve you problem with building a data annotation package (see below)?
 
I am trying to do something similiar, although not with an affy chip, and I get the same error as you:
 
'no direct or inherited method for function 'baseFile<-' for this call'
 
Kind regards,
Henrik Hornshøj
 
Department of Genetics and Biotechnology Danish Institute of Agricultural Sciences.
 
 

[BioC] affymetrix pig annotation data

Morten Mattingsdal morten.mattingsdal at student.uib.no <mailto:bioconductor%40stat.math.ethz.ch?Subject=%5BBioC%5D%20affymetrix%20pig%20annotation%20data&In-Reply-To=>
Mon Nov 14 18:28:32 CET 2005 

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________________________________

Hello open-source spirits,

Im trying to build an annotation data library for the Sus scrofa (common
pig) affymetrix chip: GeneChip® Porcine Genome Array http://www.affymetrix.com/products/arrays/specific/porcine.affx

but Im not very sucessful in doing so.. my error is

Error in "baseFile<-"(`*tmp*`, value =
"C:\\DOCUME~1\\mortema\\LOCALS~1\\Temp\\Rtmp2376\\tempFile26288") :
        no direct or inherited method for function 'baseFile<-' for this call

and I dont know what this is trying so tell me. My imput is probe ID in coloum 1 and genbank acc.nr in coloum 2.
"Ssc.11.1.S1_at"    "NM_213802.1"
and I have succesfully build packages before with human and mouse. But this is my first go at pig.

Does anyone have this library already build or can someone help me build it ?

(im deeply sorry if this is already listed in the metadata dir at bioconductor. But cant find anything related to pig)

best
morten


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