[BioC] FW: Question (vennDiagram vs. topTable) for AffylmGUI 1.3.0
smyth at wehi.edu.au
Thu Sep 29 09:21:01 CEST 2005
At 07:48 AM 23/09/2005, Luo, Wen wrote:
>Thanks for the clarification. Two more related questions:
>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.
>Thanks again for providing such a great package.
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