[BioC] problems with genome files?

[Robert Gentleman]

On Wed, Oct 20, 2004 at 04:21:26PM +0100, Manu Bi wrote:
> Dear all
>  
> I am trying to analyse some U133 plus2 generated data but I have some problems and wondered if anyone can help.
> My code lines are:
> > x <- ReadAffy(myfiles)
> > x
>  
> and I get the message:
>  
>  Note: You did not specify a download type.  Using a default value of: Win32 
> This will be fine for almost all users

  You really did not give us enough information here. What version of
  R, and of affy are you using? If you are using the release branch of
  Bioconductor you can download the data packages from the web-site
  and try to install them manually.

  If not, or if you want you can try to use reposTools directly.
  Something like:

   library(reposTools)
   install.packages2("hgu133plus2")

  should work (provided you actually do have an internet connection on
  the computer you are running the analysis on).

  Robert


>  
> Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == "")) return(NULL) : 
>         missing value where TRUE/FALSE needed
> AffyBatch object
> size of arrays=1164x1164 features (127026 kb)
> cdf=HG-U133_Plus_2 (??? affyids)
> number of samples=12
> Warning message: 
> missing cdf environment ! in: show(structure(list(), exprs = structure(c(177, 17704, 184, 17894,  
> Note: You did not specify a download type.  Using a default value of: Win32 
> This will be fine for almost all users
>  
> Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == "")) return(NULL) : 
>         missing value where TRUE/FALSE needed
> 
>  
> could anyone tell me what am I doing wrong?
>  
> thank you
>  
> M
> 
> 		
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
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