Hi, folks, Has anybody done any comparison between Affymetrics and Nimblegen? It seems that there is more packages for Affymetrics in Bioconductor but not that much for Nimblegen. Should I stick with Affymetrics or Nimblegen? Thank you very much! Nicole --

Hi Nicole, in case you intend to do ChIP-chip you might find some anwers in here http://www.ncbi.nlm.nih.gov/pubmed/18258921 my personal point of view: the array tech of nimblegen can be considered superior. i also prefer two-color arrays (nimblegen) as the analysis is more straight forward. apart from reading the raw data files you don't need specific bioconductor packages as the analysis (normalization, significance testing, enrichment localization) can be done with rather (simple) general routines (imho). i would go for nimblegen. but i agree with the authors in the abovementioned publication: it is rather NOT the array technology which is the most crucial factor in ChIP-chip but e.g. antibody, organism, cell type.. etc etc. best regards Tobias On Jun 10, 2008, at 10:55 PM, Xiaoyun(Nicole) Li wrote: > Hi, folks, > > Has anybody done any comparison between Affymetrics and Nimblegen? It > seems that there is more packages for Affymetrics in Bioconductor > but not > that much for Nimblegen. Should I stick with Affymetrics or Nimblegen? > > Thank you very much! > > Nicole > > -- ====================================================================== Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany