[BioC] building annotation package for porcine

[Fraser Sim]

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 Pérez 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
>
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