Yes. And if you don't like the warning, just change groups to group. Jim On 6/12/2014 3:55 PM, Chinh Hoan wrote: > Thanks Jim, > This means that I still can process the data as usual? silly me. Again I highly appreciate your response. > Chinh > ________________________________________ > From: James W. MacDonald [jmacdon at uw.edu] > Sent: Thursday, June 12, 2014 2:49 PM > To: Chinh Hoan; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] readDGE > > Hi Chinh Hoan, > > On 6/12/2014 11:36 AM, Chinh Hoan wrote: >> Hello all, >> Below is my problem with readDGE. Could you please tell what should I do to fix the problem? thanks! >> Chinh >> targets <- readTargets() >> targets >> files groups description >> 1 S3WT_tophatcount.txt CT TAM >> 2 S4WT_tophatcount.txt CT TAM >> 3 S1lrh1KO_tophatcount.txt KO TAM >> 4 S2lrh1KO_tophatcount.txt KO TAM >>> y <- readDGE(targets) >> Warning messages: >> 1: In `$.data.frame`(x$samples, group) : >> Name partially matched in data frame >> 2: In `$.data.frame`(x$samples, group) : >> Name partially matched in data frame > > If you look at ?readDGE, under the files argument, there is this: > > files: character vector of filenames, or alternatively a data.frame > with a column containing the file names of the files > containing the libraries of counts and, optionally, columns > containing the ?group? to which each library belongs, > descriptions of the other samples and other information. > > And what that means is that a column labeled 'group' will be used to say > which group the library belongs to. Since you have a column labeled > 'groups', R is matching to that, and giving you a warning to let you > know that it is matching to something that isn't an exact match, in case > it isn't what you want. If you change the targets file to have a 'group' > column, the warnings will go away. > > Best, > > Jim > > > > >> >> ________________________________ >> >> UT Southwestern Medical Center >> The future of medicine, today. >> >> _______________________________________________ >> 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 >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099