Hi Kenny,

Thanks for your interest in UPC.

The Python version can be downloaded from here: http://jlab.bu.edu/software/scan-upc/. If you decide to use this version, let me know, and I will tell you how to extract the UPC values.

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:

library(SCAN.UPC)
?UPC

Let me know if you have any questions about it.

Regards,
-Steve

From: "W. Evan Johnson" <wevanjohnson@gmail.com<mailto:wevanjohnson@gmail.com>>
Date: Wednesday, November 7, 2012 Wed, Nov 7, 2011 2:59 PM
To: Kenny Daily <kmdaily@gmail.com<mailto:kmdaily@gmail.com>>, Stephen Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>>
Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>
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?

Thanks!

Evan



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?

Cheers,

Kenny

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