[BioC] Nimblegen chip data analysis

[Sean Davis]

Not sure why this popped up again, but I stand corrected on the two-color
point.  Nimblegen has probesets similar to affy design, as pointed out in a
post earlier today.

Sean

----- Original Message -----
From: "Sean Davis" <sdavis2 at mail.nih.gov>
To: <bioconductor at stat.math.ethz.ch>; "Andrew Kern" <adkern at ucdavis.edu>
Sent: Saturday, August 28, 2004 9:03 AM
Subject: Re: [BioC] Nimblegen chip data analysis


> Andrew,
>
> Nimblegen is just two-color data, but on a grand scale.  I would look at
> limma or marray packages, but if you have a custom array for a specialized
> purpose, other packages may be more appropriate.  You will have to read
the
> data yourself, so you will probably have to learn to use read.table (see
> 'Introduction to R manual' and 'R data import/export', both on the CRAN
> site).  (There is not a package for reading Nimblegen data.)
>
> Sean
>
> ----- Original Message -----
> From: "Andrew Kern" <adkern at ucdavis.edu>
> To: <bioconductor at stat.math.ethz.ch>
> Sent: Friday, August 27, 2004 5:51 PM
> Subject: [BioC] Nimblegen chip data analysis
>
>
> > 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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>
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