[BioC] comparing method

[Naomi Altman]

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)
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