[BioC] annaffy can't saveHTML

[James W. MacDonald]

Hi Assa,

Assa Yeroslaviz wrote:
> Hello everybody,
> 
> I try to save my result from various microarry experiments as annotated HTML
> files.
> Unfortunately I have some problems with the data from Arabidopsis plants.
> 
> my script is as such:
> require("annaffy")
>     genenames<-rownames(x$resultset)
>     annotation.db <- paste(x$annotation,".db",sep="")
>     atab<-aafTableAnn(genenames,annotation.db,aaf.handler()[c(1:3)]) # just
> an example
>     filename<-paste("aafTable_",x$tableType,".html",sep="")
>     saveHTML(atab,file=filename)
> 
> i tried in on two data sets. one from Zebrafish which works perfectly fine
> and one from Arabidopsis.
> 
> Unfortunately I'm getting some troubles with the ATH data set. Trying to
> save is as a HTML file doesn't seems to work. I get the following error
> message:
> (German) Fehler in nchar(text <- getText(object)) :
>   ungültige multibyte Zeichenkette 1
> (translated) error in nchar(text <- getText(object)) :
>   invalid multibyte string 1
> 
> Can anyone tell me waht kind of an error is that? I just can't understand
> why it doesn't work.

Well, that isn't the most helpful error message I have ever seen.

Load the org.At.tair.db package (which all Arabidopsis chip level 
packages are based on), and then do:

ls("package:org.At.tair.db")

Then compare the output to

aaf.handler()[1:3]

You will see that you are asking annaffy to annotate something that 
doesn't exist for the Arabidopsis annotation packages.

Best,

Jim

> 
> Thx for your help
> 
> Assa
> 
> 
> 
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