[BioC] add a gene symbol colums in an exprSet or a matrix / infinite recursion error message

[Florence Combes]

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 <- getSYMBOL(affy.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 écrit:
>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 at 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 at jimmy.harvard.edu        |
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