Hi Sean, I just saw your message after sending the last one a minute ago. My question was that I wanted to use a character object 'gplaccess' that contained the string "gpldata$GPL96" I wanted to use this string to access a data.frame in a GEOData object, but the Table() function expects a GEOData-Class, not a string. So Table(gpldata$GPL96) will access the data.frame but Table(gplaccess) would not access that data.frame, as I get the following error: > Table(gplaccess) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "character" So, is there a function I can apply to 'gplaccess' to have it be an accepted argument to Table()? I tried Table(cat(gplaccess)) Tableas.name(gplaccess)) and others without success. Thanks again, Jeremiah On Tue, Jun 29, 2010 at 6:47 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > Hi, Jeremiah. > > The gpldata object is a list and the line that you are using that you say > does work is the correct way to access the data.? I'm not sure what else you > are trying to do.? Could you clarify? > > Sean > > On Jun 29, 2010 7:44 PM, "Jeremiah H. Savage" <jeremiahsavage at="" gmail.com=""> > wrote: > > Hello, > > I would like to get the Table information out of multiple GPLList objects. > > How can I use a string/char variable as a function argument? > > In this case the function is GEOquery::Table() > > geodata <- parseGEO("GSExxxx.soft") > gpldata <- GPLList(geodata)[1] > gplname <- names(gpldata) ?# eg. "GPL96" > gplaccess <- paste(gpldata,gplname,sep="$") > > ENTREZ_GENE_ID <- Table(gplaccess)$ENTREZ_GENE_ID > ###^^^ the above line does NOT work ,but > > ENTREZ_GENE_ID <-Table(gpldata$GPL96)$ENTREZ_GENE_ID > ###^^^ the above line DOES work > > _______________________________________________ > 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 >

That does work. Thanks. I also was pointed to a way to do the function call using a string to represent the entire argument: gplaccess <- "gpldata$GPL97" Table(eval(parse(text=gplaccess))) Jeremiah On Wed, Jun 30, 2010 at 3:36 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > You can also do gpldata[["GPL96"]].? Is that what you want to do? > > Sean > > On Jun 29, 2010 10:06 PM, "Jeremiah H. Savage" <jeremiahsavage at="" gmail.com=""> > wrote: > > I just found out that I can access the gpldata list object through > [[1]] instead of $GPL96, so the problem is solved. > > On Tue, Jun 29, 2010 at 4:44 PM, Jeremiah H. Savage > <jeremiahsavage at="" gmail.com=""> wrote: >> Hello, >> >> ...