Thanks for your answer. It gives in http://affycomp.jhsph.edu/faq.html a R-Script. The file is called "affycomp.R". At the beginning of this file is written: affycomp.info <- read.table("info.txt",sep="\t",as.is=TRUE,quote="") method.name <- affycomp.info[3,2] When I start this script in R, I get: > source("./R/ME_R/affycomp.R") >>Error in file(file, "r") : unable to open connection >>In addition: Warning message: >>cannot open file `info.txt' When I delete 2 lines and write method.name=NULL, I get: > source("./R/ME_R/affycomp_irri.R") Performing 6 assessments that will take a few minutes...... Performing 3 assessments that will take a few seconds... Writing to file spike-in-133-assessment.tex Processing code chunks ... 1 : term hide 2 : term verbatim Error: chunk 2 Error in nrowaffycomp.info) : Unable to find the argument "x" in selecting a method for function "nrow" I believe that I must "info.txt" at the beginning of the program given. But I can't "info.txt" finden! Or these error messages have other solution? Thanks, Mohammad "Harris A. Jaffee" <hjaffee@jhmi.edu> schrieb am 19.05.05 18:34:15: > > >---------- Forwarded message ---------- > >Date: Thu, 19 May 2005 15:01:58 +0200 > >From: Mohammad Esad-Djou <shahrgol@web.de> > >To: bioconductor@stat.math.ethz.ch, rafa@jhu.edu, ririzarr@jhsph.edu > >Subject: affycomp and info.txt? > > > >but affycomp.R needs "info.txt" file. > >where can I find info.txt? > > It's built from the information supplied in the submission form. Here > is an example: > > fullname: Rafael A. Irizarry > method: MAS 5.0 > nickname: MAS 5.0 > competition: YES > URL: http://www.affymetrix.com/support/technical/technotes/statis tical_algorithms_technote.pdf > > If competition==YES, these values later appear in an index.html file that > is obtained by clicking on a Method/Submitter value in one of the results > tables. For example, the link "MAS 5.0/rafa" goes to this page: > > http://affycomp.biostat.jhsph.edu/AFFY2/rafa@jhu.edu/030424.1033/ > > To get the affycomp package itself, go to: > > http://www.bioconductor.org/repository/devel/package/html/affyc omp.html > > Let me know if I can be of further help. -Harris

> If you have a valid info.txt file, something like I sent you, I do not have a valid file. can you send to me please as attachment? Afterwards I can use the file as sample. Thanks, Mohammad > > If you have a valid info.txt file, something like I sent you, and you > execute these commands in R: > > > affycomp.info <- read.table("info.txt",sep="\t",as.is=TRUE,quote="") > > affycomp.info > > you should see something like: > > V1 > 1 fullname: > 2 method: > 3 nickname: > 4 competition: > 5 URL: > V2 > 1 Rafael A. Irizarry > 2 MAS 5.0 > 3 MAS 5.0 > 4 YES > 5 http://www.affymetrix.com/support/technical/technotes/statistical_ algorithms_technote.pdf > > Do not proceed until you have this. > > > When I delete 2 lines and write method.name=NULL, I get: > >> source("./R/ME_R/affycomp_irri.R") > > Performing 6 assessments that will take a few minutes...... > > Performing 3 assessments that will take a few seconds... > > Writing to file spike-in-133-assessment.tex > > Processing code chunks ... > > 1 : term hide > > 2 : term verbatim > > > > Error: chunk 2 > > Error in nrowaffycomp.info) : Unable to find the argument "x" in selecting a method for function "nrow" > > I believe that I must "info.txt" at the beginning of the program given. > > Absolutely!