R help - Apr 2010 - hugene10stv1cdf

Hi all,
I'm just tried to start analysing some micro-array chips. And R was
asking for this package. When I tried to install it it says that:

Using R version 2.10.1, biocinstall version 2.5.10.
Installing Bioconductor version 2.5 packages:
[1] "hugene10stv1cdf"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ?hugene10stv1cdf? is not available

What do I wrong and where can I get this package from?

Thanks

Christoph

On 04/15/2010 08:43 PM, Christoph Knapp wrote:
> Hi all,
> I'm just tried to start analysing some micro-array chips. And R was
> asking for this package. When I tried to install it it says that:
> 
> Using R version 2.10.1, biocinstall version 2.5.10.
> Installing Bioconductor version 2.5 packages:
> [1] "hugene10stv1cdf"
> Please wait...
> 
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package ?hugene10stv1cdf? is not available
> 
> What do I wrong 
Ask questions about bioconductor packages on the Bioconductor mailing list.

  http://bioconductor.org/docs/mailList.html

From

  http://bioconductor.org/packages/release/AnnotationData.html

I suspect you want

  biocLite('hugene10stv1.r3cdf')

This thread

  https://stat.ethz.ch/pipermail/bioconductor/2010-April/032704.html

might also be relevant.

Martin


> and where can I get this package from?
> 
> Thanks
> 
> Christoph
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

Hi Christoph,

Christoph Knapp wrote:
> Hi all,
> I'm just tried to start analysing some micro-array chips. And R was
> asking for this package. When I tried to install it it says that:
> 
> Using R version 2.10.1, biocinstall version 2.5.10.
> Installing Bioconductor version 2.5 packages:
> [1] "hugene10stv1cdf"
> Please wait...
> 
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package ?hugene10stv1cdf? is not available
> 
> What do I wrong and where can I get this package from?
This is a Bioconductor package, so the correct list to ask this is the 
Bioconductor-help list, not R-help.

But what you want is

dat <- ReadAffy(cdfname="hugene10stv1.r3cdf")

and go from there. Affy has the unfortunate habit of naming related data 
with inconsistent names, and when I built this package last time I 
didn't notice the inconsistency.

Best,

Jim

> 
> Thanks
> 
> Christoph
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used
for urgent or sensitive issues