bioconductor-scan.upc¶
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.
| Home | http://bioconductor.org/packages/3.7/bioc/html/SCAN.UPC.html |
| Versions | 2.18.0, 2.20.0, 2.22.0 |
| License | MIT |
| Recipe | https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-scan.upc |
| Links | biotools: scan.upc |
Installation¶
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-scan.upc
and update with:
conda update bioconductor-scan.upc
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-scan.upc.
Link to this page¶
Render an 
badge with the following Markdown:
[](http://bioconda.github.io/recipes/bioconductor-scan.upc/README.html)
