[BioC] Description of affy paper by Gautier, Irizarry, Cope and Bolstad, 2005

[Ting-Yuan Liu]

Hi Greg,

This is because ReadAffy() cannot find the CEL files in the working 
directory.  The package affy doesn't provide CEL files, so you have to 
find some CEL files by your own if you want to try the ReadAffy function.  

Check GEO website.  You can find some CEL files there.

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Thu, 9 Feb 2006, Alvord, Greg (DMS) [Contr] wrote:

>             Hi All: 
> 
>  
> 
>             I am completely new at Bioconductor and R, but am trying to
> learn about microarray analysis.  
> 
>  
> 
>             I am running R-2.2.1 under Windows XP, and have downloaded
> Bioconductor.
> 
>  
> 
>             To begin, I want to work through paper cited above.  But I
> am not able to access the data.
> 
>  
> 
>             I did successfully access the affy package with the command:
> 
>  
> 
> > library(affy) 
> 
> Loading required package: Biobase
> 
> Loading required package: tools
> 
>  
> 
> Welcome to Bioconductor 
> 
>  
> 
>         Vignettes contain introductory material.
> 
>         To view, simply type 'openVignette()' or start with
> 'help(Biobase)'. 
> 
>         For details on reading vignettes, see the openVignette help
> page.
> 
>  
> 
> But when I attempt to access the data on page 4 of the document, I get
> an error:
> 
>  
> 
> > Data <- ReadAffy()
> 
> Error in AllButCelsForReadAffy(..., filenames = filenames, widget =
> widget,  : 
> 
>         No cel filennames specified and no cel files in specified
> directory:C:/Program Files/R/R-2.2.1
> 
>  
> 
>             Can anyone help me enter the correct commands, or help me
> with the correct commands to download/access the information needed to
> continue working through the paper?
> 
>  
> 
> Thank you very much in advance.  
> 
>  
> 
>             Greg 
> 
>  
> 
> W. Gregory Alvord, Ph.D.
> 
> Director, Statistical Consulting Services
> 
> Computer and Statistical Services
> 
> National Cancer Institute at Frederick
> 
> Fort Detrick at 7th Street
> 
> Post Office Box B
> 
> Miller Drive, Building 362, Room 33
> 
> Frederick, MD  21702-1201
> 
> Phone:  301.846.5101
> 
> Fax:  301.846.6196
> 
> E-mail:  gwa at css.ncifcrf.gov
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>