Dear List, I have quite a big problem but probably a 'naive' question for you. I need to know if there is a good and broadly accepted way to select genes that are not differentially expressed in a microarray experiment. I am looking for a measure of the significance for the potential 'not differentially expressed' call that could be given to a gene and that can be considered reliable from the community. I have searched the internet but found just a couple of discussions and papers about selecting control genes (i.e. housekeeping) for real time pcr verification of microarrays results, but nothing more. Thanks Mike

There is not. --Naomi At 05:36 AM 5/9/2006, Mike Ferker wrote: >Dear List, > >I have quite a big problem but probably a 'naive' >question for you. > >I need to know if there is a good and broadly accepted >way to select genes that are not differentially expressed >in a microarray experiment. >I am looking for a measure of the significance for the potential >'not differentially expressed' call that could be given to a gene >and that can be considered reliable from the community. > >I have searched the internet but found just a couple of discussions >and papers about selecting control genes (i.e. housekeeping) >for real time pcr verification of microarrays results, but >nothing more. > >Thanks > >Mike > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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

Hello Naomi, now I have a question. :) > >I am looking for a measure of the significance for the potential > >'not differentially expressed' call that could be given to a gene > >and that can be considered reliable from the community. I believe that you can find with multiple Testing (e.g. SAM, siggenes) 'not differentially expressed' genes. If H0 is correct: genes are not differentially expressed. did I understand correctly? I am not sure, but I believe that multiple Testing is helpful. Thanks, Mohammad > -----Urspr?ngliche Nachricht----- > Von: Naomi Altman <naomi at="" stat.psu.edu=""> > Gesendet: 09.05.06 23:15:28 > An: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] Significancy of not differentially expressed genes > There is not. > > --Naomi > > At 05:36 AM 5/9/2006, Mike Ferker wrote: > >Dear List, > > > >I have quite a big problem but probably a 'naive' > >question for you. > > > >I need to know if there is a good and broadly accepted > >way to select genes that are not differentially expressed > >in a microarray experiment. > >I am looking for a measure of the significance for the potential > >'not differentially expressed' call that could be given to a gene > >and that can be considered reliable from the community. > > > >I have searched the internet but found just a couple of discussions > >and papers about selecting control genes (i.e. housekeeping) > >for real time pcr verification of microarrays results, but > >nothing more. > > > >Thanks > > > >Mike > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > 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 > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor