Hello all, Wondering whether there already a tried and tested solution in R to deal with the issue of mistaken identifiers [Zeeberg et al. (2004) Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics; BMC Bioinformatics]. After analysing data, I often do write.csv () and the output file is then shared to be often looked at using MS Excel. Thank you. Cheers, Chintanu [[alternative HTML version deleted]]

Hi, On Sun, Nov 11, 2012 at 11:22 PM, Chintanu <chintanu at="" gmail.com=""> wrote: > Hello all, > > Wondering whether there already a tried and tested solution in R to deal > with the issue of mistaken identifiers [Zeeberg et al. (2004) Mistaken > Identifiers: Gene name errors can be introduced inadvertently when using > Excel in bioinformatics; BMC Bioinformatics]. After analysing data, I often > do write.csv () and the output file is then shared to be often looked at > using MS Excel. I'd be surprised if you'll find a better solution than just informing people downstream to turn off the auto-correct feature. Perhaps putting together small tutorials for different platforms/versions that step people through the process of disabling this "feature" would be handy -- and perhaps it might be handier to put on a wiki some where for the better good of humanity. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

You can prevent the identifiers from being converted by using the excel file import wizard, changing gene name columns from general format to text. You could also try this: #from CRAN library(xlsx) wb <- createWorkbook() sheet <- createSheet(wb, sheetName="CellBlock") datframe <- data.frame(cbind(1:3, c("March1", "Sept1", "Hbb"))) addDataFrame(datframe, sheet, col.names=F, row.names=F, startRow=1, startColumn=1, colStyle=NULL, colnamesStyle=NULL, rownamesStyle=NULL, showNA=FALSE, characterNA="", byrow=FALSE) saveWorkbook(wb, "junk.xlsx") The output format for all cells seems to be a string with gene symbols intact. It should be possible to set column formats to text, but I couldn't get it to work. Vince ===================================================== Thank you - Tim and Steve. The link looks interesting. Correcting at one's end doesn't end the problem being Excel a widely used spreadsheet program - because 'people will turn around and send it back to you" again (as Tim rightly points out). Further, it also seems that it is impossible to effectively disable this feature in Excel (i.e., disabling this specific autocorrection in Excel). Cheers, Chintanu ===================================================== On Tue, Nov 13, 2012 at 5:11 AM, Tim Triche, Jr. <tim.triche at="" gmail.com="">wrote: > Be surprised :-) > > http://cran.r-project.org/web/packages/HGNChelper/index.html > > The trouble with anything readable by Excel is that people will turn > around and send it back to you. Including vendors > > > On Sun, Nov 11, 2012 at 8:50 PM, Steve Lianoglou < > mailinglist.honeypot at gmail.com> wrote: > >> Hi, >> >> On Sun, Nov 11, 2012 at 11:22 PM, Chintanu <chintanu at="" gmail.com=""> wrote: >> > Hello all, >> > >> > Wondering whether there already a tried and tested solution in R to deal >> > with the issue of mistaken identifiers [Zeeberg et al. (2004) Mistaken >> > Identifiers: Gene name errors can be introduced inadvertently when using >> > Excel in bioinformatics; BMC Bioinformatics]. After analysing data, I >> often >> > do write.csv () and the output file is then shared to be often looked at >> > using MS Excel. >> >> I'd be surprised if you'll find a better solution than just informing >> people downstream to turn off the auto-correct feature. >> >> Perhaps putting together small tutorials for different >> platforms/versions that step people through the process of disabling >> this "feature" would be handy -- and perhaps it might be handier to >> put on a wiki some where for the better good of humanity. >> >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > [[alternative HTML version deleted]]