[BioC] Access to Affy chip annotation data in affylmGUI

[Seth Falcon]

On 16 Jan 2006, parryl3 at cardiff.ac.uk wrote:

> Users,
>
> My install of affylmGUI works as expected apart from when I try to
> obtain results and reports.  It gives me the error below and then
> just displays the probe ID in the output instead of gene names.
>
> Has the location of the file changed or can I specify a way of
> finding it?
>
> [1] "Attempting to download mouse4302 from
> http://www.bioconductor.org/packages/data/annotation/1.7/" Error in
> download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method =
> method) : cannot open URL
> 'http://www.bioconductor.org/packages/data/annotation/1.7//mouse4302_1.6.9.zip'
> In addition: Warning message: cannot open: HTTP status was '404 Not
> Found' Note: Using download type: Win32
>
> Any ideas?

I'm not sure how affylmGUI is trying find packages, but it seems to be
confused about their location.  The annotation package would never
have been at the URL listed.

You can install the mouse4302 annotation data package (and any other
Bioconductor package) using the following R commands:

  source("http://bioconductor.org/biocLite.R")
  biocLite("mouse4302")

Hopefully that will get you going.  In the meantime, we will try to
figure out what's going on with affylmGUI for package installation.
Thanks for the report!

Best,

+ seth