[BioC] comparing method
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:
>>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)
>Dept. of Statistics 814-863-7114 (fax)
>Penn State University 814-865-1348 (Statistics)
>University Park, PA 16802-2111
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