Re: [R] expression matrix

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Sat, 08 Mar 2008 06:09:22 -0800

Christophe -- You'll want to coerce golubMerge to an ExpressionSet.

> library(Biobase)
> library(golubEsets)
> data(golubMerge)
> golubUpdated <- as(golubMerge, "ExpressionSet")
Warning messages:
1: In asMethod(object) :
  missing or mis-shaped 'se.exprs' in original object; creating ExpressionSet without se.exprs 2: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 3: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead

The warning messages above can, in this case, be ignored. After this, everything should be fine, e.g.,

> exprs <- exprs(golubUpdated)

Martin

"Douglas Bates" <bates_at_stat.wisc.edu> writes:

> On Sat, Mar 8, 2008 at 7:00 AM, Keizer_71 <christophe.lo@gmail.com> wrote:
>
>> Hello,
>
>> I am to run this R script but i keep getting this error.

>
>> > expr<-exprs(golubMerge)
>> Warning message:
>> The exprSet class is deprecated, use ExpressionSet instead
>
>> I tried to find information on the website but no luck. (exprSet...etc)
>
> I think you want to try the Bioconductor (http://www.bioconductor.org)
> web site instead of the R web site.
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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Received on Sat 08 Mar 2008 - 14:17:22 GMT

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