[BioC] Convert gene expression matrix to ExpressionSet

[Martin Morgan]

On 11/06/2011 08:23 PM, Wendy Qiao wrote:
> Thanks a lot, Martin.
>
> It is a good idea. The example in section 4.1 seems exactly what I want,
> but it gives the following error. I wonder if you have any insight about
> this error. have checked Biobase manual. "ExpressionSet" is a valid
> function. I was wondering if you have any insight. Thank you very much.
>
>
>  > library("Biobase")
>  > dataDirectory <- system.file("extdata", package="Biobase")
>  > exprsFile <- file.path(dataDirectory, "exprsData.txt")
>  > exprs <- as.matrix(read.table(exprsFile, header=TRUE,
> sep="\t",row.names=1,as.is <http://as.is>=TRUE))
>  > minimalSet <- ExpressionSet(assayData=exprs)
> Error: could not find function "ExpressionSet"

Hi Wendy --

You are using an older version of R and / or Biobase. Update R (to 
version 2.14.0 and Bioconductor

   http://bioconductor.org/install/

or consult the version of the vignette appropriate for your version of 
Biobase

   browseVignettes("Biobase")

Martin

>
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> Wendy
>
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> On 6 November 2011 23:04, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     On 11/06/2011 07:29 PM, Wendy Qiao wrote:
>
>         Hi all,
>
>         I would like to use the GSVA package on my data. In order to do
>         this, the
>         gene expression matrix has to be converted into a ExpressionSet.
>         Does
>         anybody know a function for this purpose? I found an example
>         from the
>         "Convert Data Objects" page (
>         http://rss.acs.unt.edu/Rdoc/__library/convert/html/coerce.__html
>         <http://rss.acs.unt.edu/Rdoc/library/convert/html/coerce.html>). The
>         following code in the example gives me an error, but I am not
>         sure how to
>         define a new class. Could anybody help? Thank you very much.
>
>         maT = new("marrayInfo", maLabels=c("S1", "S2"),
>            maInfo= testTarget)
>
>         Error in getClass(Class, where = topenv(parent.frame())) :
>         "marrayInfo" is not a defined class
>
>
>     Hi Wendy -- have you looked at the Biobase vignette 'An Introduction
>     to Biobase and ExpressionSet' at
>
>     http://bioconductor.org/__packages/release/bioc/html/__Biobase.html
>     <http://bioconductor.org/packages/release/bioc/html/Biobase.html>
>
>     ?
>
>     Martin
>
>
>         Wendy
>
>                 [[alternative HTML version deleted]]
>
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>     --
>     Computational Biology
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
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>
>


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

Location: M1-B861
Telephone: 206 667-2793