- Label
- SCAN / UPC
- Package
- SCAN.UPC
- Title
- Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
- Description
- SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.
Piccolo SR, Withers MR, Francis OE, Bild AH and Johnson WE (2013). βMulti-platform single-sample estimates of transcriptional activation.β Proceedings of the National Academy of Sciences of the United States of America, 110(44), pp. 17778-17783. doi: 10.1016/j.ygeno.2012.08.003.