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List:       bioconductor
Subject:    Re: [BioC] FW: Question (vennDiagram vs. topTable) for AffylmGUI
From:       Gordon Smyth <smyth () wehi ! edu ! au>
Date:       2005-09-29 7:21:01
Message-ID: 6.2.1.2.1.20050929171014.021da158 () imaphost ! wehi ! edu ! au
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At 07:48 AM 23/09/2005, Luo, Wen wrote:
>Hi Gordon,
>
>Thanks for the clarification. Two more related questions:
>
>decideTests(object,method="separate",adjust.method="fdr",p.value=0.05)
>is the default for command-line limma decideTests?
>
>What are the defaut method and adjust.method for affylmGUI?

The method used by limmaGUI and afflmGUI is equivalent to the command line

   decideTests(object, method="nestedF", adjust="none", p.value=0.01)

In other words, it is based on the older command classifyTestsF().

>Is there a reference which elaborates other methods such as
>'"heirarchical"' (adjusts down genes and then across
>      contrasts is given from the help menu)?

I don't know of any papers at all yet on multiple testing for microarray 
linear models (i.e., for multple linear models). The methods implemented in 
limma do not yet have any further documentation.

Gordon

>Thanks again for providing such a great package.
>
>Wen


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