[BioC] annaffy can't saveHTML
James W. MacDonald
jmacdon at med.umich.edu
Tue Feb 16 15:45:21 CET 2010
Err. Sys.setlocale(locale = "C")
Note that you _could_ have found this using apropos:
> apropos("locale")
[1] "localeToCharset" "Sys.getlocale" "Sys.localeconv" "Sys.setlocale"
So my random brain dumps can sometimes be used to find the actual
function ;-D
Best,
Jim
Assa Yeroslaviz wrote:
> 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
> <mailto: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 <mailto: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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>
>
>
>
> --
> Assa Yeroslaviz
> Kockelsberg 22
> 51371 Leverkusen
> Sent from Dusseldorf, NW, Germany
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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