[BioC] Re: affycomp and info.txt? (fwd)

[Mohammad Esad-Djou]

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 nrow(affycomp.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 at 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 at web.de>
> >To: bioconductor at stat.math.ethz.ch, rafa at jhu.edu, ririzarr at 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/statistical_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/affycomp.html
> 
> Let me know if I can be of further help.  -Harris