[BioC] annaffy can't saveHTML

[James W. MacDonald]

Hi Assa,

Assa Yeroslaviz wrote:
> Hello James,
> 
> thanks for the answer but it didn't solve my problem.
> 
> I don't have a problem with the annotations. These are the columns from
> aaf.handler. I don't try to re-map them.

True enough. I forgot that annaffy remaps DESCRIPTION to GENENAME in the 
case of A. thaliana, and other annotation packages that don't have a 
DESCRIPTION table.

> 
> The problem comes up when I'm trying to save the list in HTML format. theer
> are two genes in the list, which have something in the descriptions column
> which R can't work with. I narrowed it down to this two cells
>> atab[127,]
> An object of class “aafTable”
> Slot "probeids":
> [1] "255891_at"
> 
> Slot "table":
> $Description
> An object of class "aafList"
> [[1]]
> [1] "S2P-like putative metalloprotease, also contain transmembrane helices
> near their C-termini and many of them, five of seven, contain a conserved
> zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY-like
> proteins share two additional highly conserved motifs, the previously
> reported NPDG motif (aa 442\x96454 in EGY1, Rudner et al., 1999) and a newly
> defined GNLR motif (aa 171\x96179 in EGY1). The GNLR motif is a novel
> signature motif unique to EGY1 and EGY-like proteins as well as other EGY1
> orthologs found in cyanobacteria."
> [2] "S2P-like putative metalloprotease, also contain transmembrane helices
> near their C-termini and many of them, five of seven, contain a conserved
> zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY-like
> proteins share two additional highly conserved motifs, the previously
> reported NPDG motif (aa 442\x96454 in EGY1, Rudner et al., 1999) and a newly
> defined GNLR motif (aa 171\x96179 in EGY1). The GNLR motif is a novel
> signature motif unique to EGY1 and EGY-like proteins as well as other EGY1
> orthologs found in cyanobacteria."
> attr(,"class")
> [1] "aafDescription"
> 
> the problem is in the description cloumn with the \x96  ["... motif  (aa
> 171\x96179 in EGY1)..."] coding. But I don't understand why the aanotation
> uses it.

Not sure what you are getting at here - you asked for these data and got 
them. But the problem arises not in annaffy, but in base R, because 
\x96454 isn't a valid multibyte string in UTF-8 (and neither is \x96179 
for that matter).

The fix is simple:

Set.syslocale(locale = "C")

then on with the show!

Best,

Jim


> 
> I'm not sure where I can change the coding of my R output (RKWard 0.4.9b
> with KDE 3.5.10), but at least i know it's not the data that making the
> problems.
> 
> If anyone has an Idea on how to set this right, I'll be pleased.
> 
> THX
> 
> Assa
> 
> On Wed, Feb 10, 2010 at 17:02, James W. MacDonald <jmacdon at med.umich.edu>wrote:
> 
>> 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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