[BioC] comparing method

Nate King mybioconductor at hotmail.com
Mon Jan 23 22:18:59 CET 2006

thank you very much for the superfast answer. after nearly giving up I 
finally found a method to count the genes of both groups using 
vennDiagramms. this is of course not very elegant.

your method is just perfect and much more elegant. thanks very much!


>From: Naomi Altman <naomi at stat.psu.edu>
>To: "Nate King" <mybioconductor at hotmail.com>,bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] comparing method
>Date: Mon, 23 Jan 2006 15:43:57 -0500
>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.
>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.
>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 
>>Thanks very much in advance!
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>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

More information about the Bioconductor mailing list