Thanks so much, Martin. It worked by updating R and Bioconductor packages!

Wendy

On 6 November 2011 23:33, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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/ <http://bioconductor.org/install/>
>
> or consult the version of the vignette appropriate for your version of
> Biobase
>
>  browseVignettes("Biobase")
>
> Martin
>
>
>>
>> Wendy
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 6 November 2011 23:04, Martin Morgan <mtmorgan@fhcrc.org
>> <mailto:mtmorgan@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>
>>        <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>
>>
>>    <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
>

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