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=TRUE))
> minimalSet <- ExpressionSet(assayData=exprs)
Error: could not find function "ExpressionSet"


Wendy












On 6 November 2011 23:04, Martin Morgan <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>).
>> 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]]
>>
>> ______________________________**_________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>

	[[alternative HTML version deleted]]

