[BioC] Nimblegen chip data analysis

[Sean Davis]

Andrew,

Nimblegen arrays are simply two-color arrays on (legal) steroids.  You can
simply treat them as such.  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).

Sean

On 8/27/04 17:51, "Andrew Kern" <adkern at 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
> 
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