[BioC] enrichment packages that accept t-stat (or related stat) as input

[Gordon K Smyth]

Dear Juliet,

Why not use the enrichment functions that are already part of the limma 
package?   See

   ?roast
   ?camera
   ?romer

and references there-in.

Best wishes
Gordon


> Message: 19
> Date: Thu, 29 Aug 2013 20:43:04 -0400
> From: Juliet Hannah <juliet.hannah at gmail.com>
> To: Robert Castelo <robert.castelo at upf.edu>
> Cc: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: Re: [BioC] enrichment packages that accept t-stat (or related
> 	stat) as input
>
> Hi Robert,
>
> Thanks for your response. I will look into it.
>
> Also is it correct GSVA always requires an expression matrix. It seems 
> that it integrates with limma, so if I have done an analysis in limma 
> does this mean that I should be able to use GSVA for an enrichment 
> analysis.
>
> Thanks,
>
> Juliet
>
>
> On Thu, Aug 29, 2013 at 2:43 AM, Robert Castelo <robert.castelo at upf.edu>wrote:
>
>> Juliet,
>>
>> i think the first 5 pages in the vignette entitled "Using Categories to
>> Analyze Microarray Data" from the Category package:
>>
>> http://www.bioconductor.org/**packages/release/bioc/html/**Category.html<http://www.bioconductor.org/packages/release/bioc/html/Category.html>
>>
>> may be doing what you are looking for.
>>
>> cheers,
>> robert.
>>
>>
>> On 08/28/2013 08:04 PM, Juliet Hannah wrote:
>>
>>> All,
>>>
>>> I am looking for an Bioconductor enrichment package that does something
>>> similar to GSEA for pre-computed test statistics. This method would not
>>> rely on a cutoff. That is, rather than passing an expression matrix, one
>>> can compute summarizes outside of the package (such as a limma t), and
>>> then
>>> pass these. Any suggestions?
>>>
>>> Thanks,
>>>
>>> Juliet
>>>
>>>         [[alternative HTML version deleted]]
>>>
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>> --
>> Robert Castelo, PhD
>> Associate Professor
>> Dept. of Experimental and Health Sciences
>> Universitat Pompeu Fabra (UPF)
>> Barcelona Biomedical Research Park (PRBB)
>> Dr Aiguader 88
>> E-08003 Barcelona, Spain
>> telf: +34.933.160.514
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>>
>

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