Dear all, I am working with affymetrix data and I am writing a program in Perl to normalize the data. I would like to use some statistical formulas from R in my Perl program, some kind of interface. How can I do this? My second question is where can I find the R package translating the affymetrix cel files with the help of affymetrix cdf file. I know that I have seen a function like this in R but now I am not able to find it. Thank you, Pauline -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Dear Pauline Maybe you mean the Raffy package from Terry Speed?s group? http://biosun01.biostat.jhsph.edu/~ririzarr/Raffy/ (However, I am not sure whether it translates CEL files, I did not test it.) Best regards Christian ---------------------------------- C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a, A.u.s.t.r.i.a Pauline Mattsson wrote:> Dear all, > > I am working with affymetrix data and I am writing a program in Perl to > normalize the data. I would like to use some statistical formulas from R in my > Perl program, some kind of interface. How can I do this? My second question is > where can I find the R package translating the affymetrix cel files with the > help of affymetrix cdf file. I know that I have seen a function like this in R > but now I am not able to find it. > > Thank you, > > Pauline > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html > Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Mon, 21 Jan 2002, Pauline Mattsson wrote:> Perl program, some kind of interface. How can I do this? My second question is > where can I find the R package translating the affymetrix cel files with the > help of affymetrix cdf file. I know that I have seen a function like this in R > but now I am not able to find it.you can find a package that includes a perl script that converts cel/cdf files into a tab delimeted file here: http://biosun01.biostat.jhsph.edu/~ririzarr/Raffy another useful package can be found here: http://www.cbs.dtu.dk/laurent/download/affyR/ a package combining these two packages that calls C to read in information from cel/cdf is coming out soon. rafael -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Hi Pauline, The RSPerl package (http://www.omegahat.org/RSPerl) provides a way to call R from Perl and Perl from R. It works for Unix and could be ported to Windows. D. Pauline Mattsson wrote:> Dear all, > > I am working with affymetrix data and I am writing a program in Perl to > normalize the data. I would like to use some statistical formulas from R in my > Perl program, some kind of interface. How can I do this? My second question is > where can I find the R package translating the affymetrix cel files with the > help of affymetrix cdf file. I know that I have seen a function like this in R > but now I am not able to find it. > > Thank you, > > Pauline > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html > Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._-- _______________________________________________________________ Duncan Temple Lang duncan at research.bell-labs.com Bell Labs, Lucent Technologies office: (908)582-3217 700 Mountain Avenue, Room 2C-259 fax: (908)582-3340 Murray Hill, NJ 07974-2070 http://cm.bell-labs.com/stat/duncan -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._