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 > > > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor

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! NK >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. > >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! >> >>NK >> >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >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 >