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
>
Alvord, Greg (DMS) [Contr] wrote:
>>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
This error indicates that you don't have any celfiles in your working
directory. If you don't have any Affy data, you will not be able to do
much with this particular vignette.
You could try some of the commands that follow this one if you first
type:
data(affybatch.example)
You could then use this AffyBatch to run some of the commands in the
vignette, such as
eset <- mas5(affybatch.example)
or
eset <- rma(affybatch.example)
etc.
HTH,
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
