[BioC] who is sam ? was: Re: comparing method

[Matthew Lyon]

where can i find explanation of the 'sam' thing? i have a pnas reference 
(Tusher, 2001)  but want a simpler explanation.

>I don't know the format of the "sam" output.  If
>you get a p-value or q-value for each gene, sort
>the lists into the same order, and count the
>number of times both values are significant.
>
>both=(p1<.05)&(p2<.05)
>sum(both)
>
>If you get a gene list from each method, there
>are is the set method, intersection, which will
>give the set of genes on both lists.  You can
>then just ask for the length of this list.
>
>--Naomi
>
>At 02:51 PM 1/23/2006, Nate King wrote:
> >Dear list,
> >
> >I am currently working on the analysis of my
> >data set and want to compare the results
> >obtained from the RMA and GCRMA routine. I´ve
> >sucessfully filtered my genes and applied the
> >"sam" function onto the filtered data sets. I
> >know want to get a ratio or count of how many
> >genes are called significant in BOTH cases. I do
> >want to compare the results. Is there a method
> >or function already to do this? Unfortunately I didn't find anything.
> >
> >Thanks very much in advance!
> >
> >NG
> >
> >
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>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
>University Park, PA 16802-2111
>
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