Search
Question: Mistaken identifiers
0
gravatar for Chintanu
5.0 years ago by
Chintanu310
Chintanu310 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. Thank you. Cheers, Chintanu [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.0 years ago by Vince Schulz60 • written 5.0 years ago by Chintanu310
0
gravatar for Steve Lianoglou
5.0 years ago by
Genentech
Steve Lianoglou12k 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
ADD COMMENTlink written 5.0 years ago by Steve Lianoglou12k
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@gmail.com> wrote: > Hi, > > On Sun, Nov 11, 2012 at 11:22 PM, Chintanu <chintanu@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@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]]
ADD REPLYlink written 5.0 years ago by Tim Triche4.2k
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@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@gmail.com> wrote: > >> Hi, >> >> On Sun, Nov 11, 2012 at 11:22 PM, Chintanu <chintanu@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@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]]
ADD REPLYlink written 5.0 years ago by Chintanu310
0
gravatar for Vince Schulz
5.0 years ago by
Vince Schulz60
United States
Vince Schulz60 wrote:
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]]
ADD COMMENTlink written 5.0 years ago by Vince Schulz60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 317 users visited in the last hour