CRAN
AssayCorrector 2.0.0
Detection and Correction of Spatial Bias in HTS Screens
Released Aug 16, 2017 by Bogdan Mazoure
Dependencies
lattice 0.20-35 kSamples 1.2-7 RColorBrewer 1.1-2 RVAideMemoire 0.9.1 latticeExtra 0.6-28
Allows to correct bias in high-throughput screening (HTS) assays. It (1) Detects plate-specific spatial bias by identifying rows and columns of all plates of the assay affected by this bias (following the results of the Mann-Whitney U test) as well as assay-specific spatial bias by identifying well locations (i.e., well positions scanned across all plates of a given assay) affected by this bias (also following the results of the Mann-Whitney U test); (2) Allows one to correct plate-specific spatial bias using either of the three additive or either of the three multiplicative PMP (Partial Mean Polish) methods (the most appropriate spatial bias model can be either specified by the user or determined by the program following the results of the Kolmogorov-Smirnov, Anderson-Darling or Cramer-von-Mises two-sample test) to correct the assay measurements as well as to correct assay-specific spatial bias by carrying out robust Z-scores within each plate of the assay and then traditional Z-scores across well locations.
Installation
Maven
This package can be included as a dependency from a Java or Scala project by including
the following your project's pom.xml file.
Read more
about embedding Renjin in JVM-based projects.
<dependencies>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>AssayCorrector</artifactId>
<version>2.0.0-b7</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>bedatadriven</id>
<name>bedatadriven public repo</name>
<url>https://nexus.bedatadriven.com/content/groups/public/</url>
</repository>
</repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:AssayCorrector')
Test Results
This package was last tested against Renjin 0.8.2504 on Oct 30, 2017.