limma (version 3.28.14)

PrintLayout: Print Layout - class

Description

A list-based class for storing information about the process used to print spots on a microarray.

PrintLayout objects can be created using getLayout. The printer component of an RGList or MAList object is of this class.

Slots/List Components

Objects of this class contains no slots but should contain the following list components:

ngrid.r:

number of grid rows on the arrays

ngrid.c:

number of grid columns on the arrays

nspot.r:

number of rows of spots in each grid

nspot.c:

number of columns of spots in each grid

ndups:

number of duplicates of each DNA clone, i.e., number of times print-head dips into each well of DNA

spacing:

number of spots between duplicate spots. Only applicable if ndups>1. spacing=1 for side-by-side spots by rows, spacing=nspot.c for side-by-side spots by columns, spacing=ngrid.r*ngrid.c*nspot.r*nspot.c/2 for duplicate spots in top and bottom halves of each array.

npins:

actual number of pins or tips on the print-head

See Also

02.Classes gives an overview of all the classes defined by this package.

Examples

#  Settings for Swirl and ApoAI example data sets in User's Guide

printer <- list(ngrid.r=4, ngrid.c=4, nspot.r=22, nspot.c=24,
                ndups=1, spacing=1, npins=16, start="topleft")

#  Typical settings at the Australian Genome Research Facility

#  Full pin set, duplicates side-by-side on same row
printer <- list(ngrid.r=12, ngrid.c=4, nspot.r=20, nspot.c=20,
                ndups=2, spacing=1, npins=48, start="topright")

#  Half pin set, duplicates in top and lower half of slide
printer <- list(ngrid.r=12, ngrid.c=4, nspot.r=20, nspot.c=20,
                ndups=2, spacing=9600, npins=24, start="topright")