On Mon, Oct 04, 2004 at 11:40:25AM +0200, Florence Combes wrote: > Dear all, > > I actually encounter an error message in relation with infinite recursion > when I try to call the write.table() function for a matrix of 288 columns > (288 hgu133a arrays ). > The error message is: > > Error: evaluation nested too deeply: infinite recursion / > options(expression=)? > > I searched the email archives and I found that I could use the command: > > options(expressions=10000) > > to solve this problem but it does not change anything. So I would like to > know if I have to increase to 20000 or more in the above line ? > Has someone already encountered same problem ??? > It looks like you may not have done what you intended to do. Can you show us a small working example (perhaps using the test data set, eset, that comes with Biobase), it is pretty hard to tell otherwise. Robert > > My goal is to add a column which includes the genesymbol before exporting > the data with write.table(). I do this with the functions > getSYMBOL > and > cbind() to add the column at the expreSet I previously transformed in a > matrix object. > > If someone know how to do that in another way which would allow me not to > encounter the error message above, please tell me.... > > Any help kindly accepted..... > > thanks a lot, > > Florence. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

OK you are right for the exemple needed. However I don't have the type of array for the Biobase eSet, so I put on this e-mail my code... eset is an exprSet for my 288 arrays. affy.id <- geneNames(eset) # to obtain the probes ID symb <- getSYMBOLaffy.id, "hgu133a") # to obtain the Gene Symbol res <- cbind(symb, exprs(eset) # to paste the Gene Symbol column with the expression data. write.table(res, fil="res.txt") It works very well for an exprSet of 10 or 20 arrays, but with 288 arrays the last line (write.table) gives the error message: Error: evaluation nested too deeply: infinite recursion / options(expression=)? Thanks for help !!! Florence. (I am working on Windows XP) Le 13:09 04/10/2004,Robert Gentleman ?crit: >On Mon, Oct 04, 2004 at 11:40:25AM +0200, Florence Combes wrote: > > Dear all, > > > > I actually encounter an error message in relation with infinite recursion > > when I try to call the write.table() function for a matrix of 288 columns > > (288 hgu133a arrays ). > > The error message is: > > > > Error: evaluation nested too deeply: infinite recursion / > > options(expression=)? > > > > I searched the email archives and I found that I could use the command: > > > > options(expressions=10000) > > > > to solve this problem but it does not change anything. So I would like to > > know if I have to increase to 20000 or more in the above line ? > > Has someone already encountered same problem ??? > > > > It looks like you may not have done what you intended to do. Can you > show us a small working example (perhaps using the test data set, > eset, that comes with Biobase), it is pretty hard to tell otherwise. > > Robert > > > > > > My goal is to add a column which includes the genesymbol before exporting > > the data with write.table(). I do this with the functions > > getSYMBOL > > and > > cbind() to add the column at the expreSet I previously transformed in a > > matrix object. > > > > If someone know how to do that in another way which would allow me not to > > encounter the error message above, please tell me.... > > > > Any help kindly accepted..... > > > > thanks a lot, > > > > Florence. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >-- >+-------------------------------------------------------------------- -------+ >| Robert Gentleman phone : (617) 632-5250 | >| Associate Professor fax: (617) 632-2444 | >| Department of Biostatistics office: M1B20 | >| Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | >+-------------------------------------------------------------------- -------+