[BioC] annaffy can't saveHTML
axel.klenk at actelion.com
axel.klenk at actelion.com
Tue Feb 16 09:51:43 CET 2010
Dear Assa,
oops, a little typo in Jim's reply:
try Sys.setlocale() instead of Set.syslocale() :-)
It is an R function and you can read its help
page to find out what is does...
Cheers,
- axel
Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland
Assa Yeroslaviz
<frymor at gmail.com
> To
Sent by: "James W. MacDonald"
bioconductor-boun <jmacdon at med.umich.edu>,
ces at stat.math.eth bioconductor at stat.math.ethz.ch
z.ch cc
Subject
02/16/2010 09:14 Re: [BioC] annaffy can't saveHTML
AM
Good morning,
Thanks again for the help.
Unfortunately I don't know what to do with this command line.
Set.syslocale(locale = "C")
Where do I need to execute it? This is not a R command and I can't find
anything in my linux to do with it.
Can you please explain to me what does this line do and how can I use it.
Thanks
Assa
On Fri, Feb 12, 2010 at 18:35, James W. MacDonald
<jmacdon at med.umich.edu>wrote:
> 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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>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
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> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
be
> used for urgent or sensitive issues
>
--
Assa Yeroslaviz
Kockelsberg 22
51371 Leverkusen
Sent from Dusseldorf, NW, Germany
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