plot.assay

Ellipsis to be passed to the <code>levelplotplot()</code> function from the <code>lattice</code> package

plate

Either "R" - raw assay, "C" - corrected assay (if it exists) or "P" - spatial bias position

type

<code>plot.assay</code> plots a hit map of the assay (only one plate at a time)

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.

plot.assay: Plot assay plate-wise

Description

Usage

Arguments

Value