| PrintLayout {limma} | R Documentation |
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.
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 |
start: | character string giving position of the spot printed first in each grid.
Choices are "topleft" or "topright" and partial matches are accepted.
|
Gordon Smyth
02.Classes gives an overview of all the classes defined by this package.
# 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")