Question: annaffy can't saveHTML
0
9.8 years ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k 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$tableType,".html",sep="") saveHTML(atab,file=filename) i tried in on two data sets. one from Zebrafish which works perfectly fine and one from Arabidopsis. Unfortunately I'm getting some troubles with the ATH data set. Trying to save is as a HTML file doesn't seems to work. I get the following error message: (German) Fehler in nchar(text <- getText(object)) : ungültige multibyte Zeichenkette 1 (translated) error in nchar(text <- getText(object)) : invalid multibyte string 1 Can anyone tell me waht kind of an error is that? I just can't understand why it doesn't work. Thx for your help Assa -- Assa Yeroslaviz Kockelsberg 22 51371 Leverkusen Sent from Dusseldorf, NW, Germany [[alternative HTML version deleted]] annotation zebrafish • 677 views ADD COMMENTlink modified 9.8 years ago by James W. MacDonald51k • written 9.8 years ago by Assa Yeroslaviz1.4k Answer: annaffy can't saveHTML 0 9.8 years ago by United States James W. MacDonald51k wrote: Hi Assa, Assa Yeroslaviz wrote: > Hello everybody, > > I try to save my result from various microarry experiments as annotated HTML > files. > Unfortunately I have some problems with the data from Arabidopsis plants. > > my script is as such: > require("annaffy") > genenames<-rownames(x$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)) : > ung?ltige 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 > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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. 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": $Description An object of class "aafList" [[1]] [1] "S2P-like putative metalloprotease, also contain transmembrane helices near their C-termini and many of them, five of seven, contain a conserved zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY- like proteins share two additional highly conserved motifs, the previously reported NPDG motif (aa 442\x96454 in EGY1, Rudner et al., 1999) and a newly defined GNLR motif (aa 171\x96179 in EGY1). The GNLR motif is a novel signature motif unique to EGY1 and EGY-like proteins as well as other EGY1 orthologs found in cyanobacteria." [2] "S2P-like putative metalloprotease, also contain transmembrane helices near their C-termini and many of them, five of seven, contain a conserved zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY- like proteins share two additional highly conserved motifs, the previously reported NPDG motif (aa 442\x96454 in EGY1, Rudner et al., 1999) and a newly defined GNLR motif (aa 171\x96179 in EGY1). The GNLR motif is a novel signature motif unique to EGY1 and EGY-like proteins as well as other EGY1 orthologs found in cyanobacteria." attr(,"class") [1] "aafDescription" the problem is in the description cloumn with the \x96 ["... motif (aa 171\x96179 in EGY1)..."] coding. But I don't understand why the aanotation uses it. I'm not sure where I can change the coding of my R output (RKWard 0.4.9b with KDE 3.5.10), but at least i know it's not the data that making the problems. If anyone has an Idea on how to set this right, I'll be pleased. THX Assa On Wed, Feb 10, 2010 at 17:02, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Assa, > > > Assa Yeroslaviz wrote: > >> Hello everybody, >> >> I try to save my result from various microarry experiments as annotated >> HTML >> files. >> Unfortunately I have some problems with the data from Arabidopsis plants. >> >> my script is as such: >> require("annaffy") >> genenames<-rownames(x$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 >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > ********************************************************** > 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 [[alternative HTML version deleted]]
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)) : >>> ung?ltige 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 >>> >>> >>> >>> ------------------------------------------------------------------ ------ >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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@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@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 >>>> >>>> >>>> >>>> ----------------------------------------------------------------- ------- >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> >>> >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > ********************************************************** > 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 [[alternative HTML version deleted]]
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)) : > ung?ltige 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 > > > > ---------------------------------------------------- -------------------- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ********************************************************** > Electronic Mail is not secure, may not be read every day, > and should not be > used for urgent or sensitive issues > > > > > > ------------------------------------------------------------ ------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ********************************************************** > 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 -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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)) : >>>> ung?ltige 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 >>>> >>>> >>>> >>>> ---------------------------------------------------------------------- -- >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> >>> >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > ********************************************************** > 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. 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