Thanks for your interest in UPC.
The Python version can be downloaded from here:
. If you decide to use this
version, let me know, and I will tell you how to extract the UPC
The R implementation is currently in the developer version of
Bioconductor. To get the development version, you'll need to install
the development version (2.16) of R first. Then if you follow the
instructions here (http://www.bioconductor.org/developers/useDevel/)
you should be able to install the SCAN.UPC development package (also
using biocLite("SCAN.UPC"). After that, you should be able to load the
package and get the help documentation using the following code:
Let me know if you have any questions about it.
From: "W. Evan Johnson"
Date: Wednesday, November 7, 2012 Wed, Nov 7, 2011 2:59 PM
To: Kenny Daily <email@example.com<mailto:firstname.lastname@example.org>>, Stephen
Subject: Re: [combat] UPC availablility
Kenny: The answer is yes. The Python version of SCAN provides both the
SCAN normalized data as well as the UPC values. We have also released
a developer version of the SCAN.UPC package that has a UPC function.
Our paper for UPC is now under review, but in all cases we are seeing
a mild to moderate performance improvement over the frma barcode.
Also, the UPC barcode works on all Affy arrays whereas the frma
version is limited.
Steve: Can you give Kenny specific instructions on how to best get UPC
values from our Python or R developer package?
On Nov 7, 2012, at 4:05 PM, Kenny Daily wrote:
Is UPC available yet for either Python or R?
How does it compare to the probabilities obtained from fRMA's barcode?
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