add a gene symbol colums in an exprSet or a matrix / infinite recursion error message
1
0
Entering edit mode
rgentleman ★ 5.5k
@rgentleman-7725
Last seen 8.9 years ago
United States
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 | +--------------------------------------------------------------------- ------+
hgu133a hgu133a • 921 views
ADD COMMENT
0
Entering edit mode
@florence-combes-906
Last seen 9.6 years ago
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 | >+-------------------------------------------------------------------- -------+
ADD COMMENT

Login before adding your answer.

Traffic: 616 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6