[BioC] Convert gene expression matrix to ExpressionSet

[Robert Castelo]

hi Wendy,

a little late, but if you consult pages 3 to 6 of the reference manual at:

http://www.bioconductor.org/packages/2.9/bioc/manuals/GSVA/man/GSVA.pdf

or the online help page of the gsva() function from the R shell with:

help(gsva)

you'll see that the gsva() function also accepts a matrix where rows 
correspond to genes and columns to samples. however, it is a very good 
practice to put your gene expression and phenotypic data into an 
ExpressionSet object to ensure integrity of both types of data. in the 
framework of the gsva() function it can also help you a lot if you're 
going to work with gene sets from the Broad Institute since the mapping 
steps between genes in the gene sets and genes in your expression matrix 
may be non-trivial for the non-experienced user and by passing an 
ExpressionSet and GeneSetCollection objects, this mapping logic will be 
seamless handled by the function. do not hesitate to post any question 
about this.

cheers,
robert.

On 11/7/11 8:13 AM, Wendy Qiao wrote:
> Thanks so much, Martin. It worked by updating R and Bioconductor packages!
>
> Wendy
>
> On 6 November 2011 23:33, Martin Morgan<mtmorgan at 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 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>
>>>         <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
>>>
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>>
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>>
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