[BioC] New Bioconductor Package: SCAN.UPC

W. Evan Johnson wej at bu.edu
Wed Oct 10 14:27:16 CEST 2012

Hey Bioconductor Users, 

I just wanted to give you all a 'heads-up' on a new package (SCAN.UPC) that appeared in last week's release of Bioconductor. In the The SCAN normalization is a new single sample Affy normalization approach that only requires information within the sample, and does not need other samples or a set of reference samples for the normalization. The great thing about this is that it means that once you normalize the array once, the normalized values won't change if other arrays are added to the expression set. This has great utility in meta-analysis and in personalized medicine applications. 

The details of our SCAN method can be found here (http://www.sciencedirect.com/science/article/pii/S0888754312001632). SCAN removes background variation and increases the signal-to-noise ratio in the samples. We are seeing instances where batch effects are removed or reduced from batches of data as well. The method is a major and uniform upgrade over RMA, and is showing slightly better or equivalent results compared to fRMA. The advantage over fRMA is that you don't need to provide a frozen reference vector for the normalization--which is difficult for some arrays and applications. Also we are seeing improved performance when combining across Affy array platforms because fRMA will need different frozen vectors for the different array platforms.  

Please let us know if you have any issues with the package. We are happy to help!


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