Dear Wolfgang, Thank you very much for your reply. I understand that I need to validate my results if I make any changes, but was not clear as to how would I do that. I like the idea of using the MA plots and am currently working on those. However, I would like your suggestion on what you think could be better in our case to identify anything as potentially differentially expressed. Should I just go with the defaults (which I think might be too conservative specifically for our condition), or should I make certain changes. I have already tried all the possible changes in parameters for estimatDispersions, and definitely see different results than default. I am currently validating all these changes, but would just like an expert view on what would be a good modification to default (if any). Kind regards, Praful Praful Aggarwal Broeckel Lab Human and Molecular Genetics Center Medical College of Wisconsin 8701 Watertown Plank Road CRI/TBRC 2nd Floor Milwaukee, WI 53226 414-955-2567 [[alternative HTML version deleted]]

Dear Praful thanks. One thing to remember is that DESeq does not do magic. It will only find what is in the data. A well-designed, sufficiently powered and carefully executed experiment is worth a lot. best wishes Wolfgang Mar/27/12 9:55 PM, Aggarwal, Praful scripsit:: > Dear Wolfgang, > > Thank you very much for your reply. I understand that I need to > validate my results if I make any changes, but was not clear as to > how would I do that. I like the idea of using the MA plots and am > currently working on those. > > However, I would like your suggestion on what you think could be > better in our case to identify anything as potentially differentially > expressed. Should I just go with the defaults (which I think might be > too conservative specifically for our condition), or should I make > certain changes. > > I have already tried all the possible changes in parameters for > estimatDispersions, and definitely see different results than > default. I am currently validating all these changes, but would just > like an expert view on what would be a good modification to default > (if any). > > Kind regards, Praful > > Praful Aggarwal Broeckel Lab Human and Molecular Genetics Center > Medical College of Wisconsin 8701 Watertown Plank Road CRI/TBRC 2nd > Floor Milwaukee, WI 53226 > > 414-955-2567 > > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > fig:phenotypiclandscape} -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber

Dear Wolfgang, Thanks a lot for your reply. Regards, Praful Praful Aggarwal Broeckel Lab Human and Molecular Genetics Center Medical College of Wisconsin 8701 Watertown Plank Road CRI/TBRC 2nd Floor Milwaukee, WI 53226 414-955-2567 [[alternative HTML version deleted]]