[BioC] Affymetrics and Nimblegen Comparison

Tobias Straub tstraub at med.uni-muenchen.de
Wed Jun 11 16:16:14 CEST 2008

Hi Nicole,

in case you intend to do ChIP-chip you might find some anwers in here

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

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

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