[BioC] question on buildChromLocation

[Martin Morgan]

Hi Alessandro --

I think this is a limitation of buildChromLocation. Most annotation
packages (e.g., hgu95av2) have  a 'map' between probe names and the
corresponding gene SYMBOL identifiers. The yeast community has gone a
different route, and uses GENENAME identifiers: the yeast packages
have yeast2GENENAME maps, rather than yeast2SYMBOL.

To get around this, I think you will need to create a copy of
buildChromLocation, e.g., by using the output of

> buildChromLocation

to define a function buildYeastChromLocation. Then edit the line near
the end to replace "SYMBOL" with "GENENAME".

Likely other parts of the package make similar kinds of assumptions.

Hope that helps,

Martin

Alessandro Fazio <fazioalessandro at hotmail.com> writes:

> Hello everybody,
>  
> I have been trying to assemble a chromLocation object by following the code in the vugnette of geneplotter package.
>  
> BUT, at the end I got this error message:
>  
>> newChrClass <- buildChromLocation("yeast2")Error in get(x, envir, mode, inherits) : variable "yeast2SYMBOL" was not found
> Even if the yeast2 package is loaded, the variable yeast2SYMBOL is not found.
>  
> Any idea to help me?
>  
> Thank you very much in advance
>  
> Alessandro Fazio
>  
>> sessionInfo()R version 2.5.0 (2007-04-23) i386-pc-mingw32 
> locale:LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
> other attached packages:      ygs98    hgu95av2      yeast2 geneplotter     lattice    annotate     Biobase    "1.16.0"    "1.16.0"    "1.16.0"    "1.14.0"    "0.15-4"    "1.14.1"    "1.14.0" 
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org