Description Slots/List Components Author(s) See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 | # 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")
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