[BioC] affymetrix pig annotation data

[Morten Mattingsdal]

Hi Henrik,

No.. I did not manage to build an annotaiton package of the affymetrix 
porcine chip, although I considered using the BLAST orthologes available 
at affymetrix.com, as input to AnnBuilder. My impression is that pig 
genes have surprisingly very poor annotaiton in public databases and 
doing micoarray on pig must be very frustrating, despite its close 
relationship to human. The annotaiton provided by Affymetrix also suck. 
(cdf file & NetAffy.)
The BLAST orthologes or Homologene could be a fruitful.. or maybe 
biomaRt & getHomolog

good luck, and mail us if you succeed :)
regards
morten


Henrik Hornshøj Jensen wrote:

>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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