Sean Davis wrote: > Andrew, > > Nimblegen arrays are simply two-color arrays on (legal) steroids. You can > simply treat them as such. Sorry, I feel like I should jump in and correct this. Most NimbleGen arrays are one-color arrays, similar to Affymetrix arrays. We do some two-color arrays, but most of it is not for expression studies. > One thing to be careful of, though, is what you assume about > differential expression if you have a highly customized array. There > aren't methods to read Nimblegen data, so you will probably have to > read it with standard R functions (read.table, for example). Decide > what hypotheses make sense for your data and think about what makes > sense for normalization (again, depends on the chip design, to some > degree). Due to the high level of customization for our array designs, we haven't invested the time to develop a specialized set of tools to load NimbleGen data into Bioconductor. I read in data with read.table and pull out row/columns as needed. Most of the Bioconductor packages have lower level functions that allow you to pass a matrix or dataframe as an argument, instead of the typical AffyBatch or expression set. It's a little more work, and sometimes a bit painful, but it does allow for lots of flexibility. Sean's point about normalization is a good one - depending on the application, you'll find that some methods of normalization are more appropriate than others. It might take a bit of experimentation to figure out which normalization method is best suited to your design/samples/application. Regards, Todd > > Sean > > On 8/27/04 17:51, "Andrew Kern" <adkern@ucdavis.edu> wrote: > > >>has anyone out there used bioconductor to analyze nimblegen >>oligonucleotide chip data? if so could you point me in the right >>direction to get me started? i've never before analyzed microarray data >>and i'm hoping to use bioconductor for this project. >>cheers, >>andrew kern >> -- ****************************************** Todd Richmond, PhD Manager of Research Informatics NimbleGen Systems, Inc. Email: todd@nimblegen.com Phone: 1-608-218-7651