getSpacing {limma}R Documentation

Get Numerical Spacing

Description

Convert character to numerical spacing measure for within-array replicate spots.

Usage

getSpacing(spacing, layout)

Arguments

spacing

character string or integer. Acceptable character strings are "columns", "rows", "subarrays" or "topbottom". Integer values are simply passed through.

layout

list containing printer layout information

Details

"rows" means that duplicate spots are printed side-by-side by rows. These will be recorded in consecutive rows in the data object.

"columns" means that duplicate spots are printed side-by-sidy by columns. These will be separated in the data object by layout$nspot.r rows.

"subarrays" means that a number of sub-arrays, with identical probes in the same arrangement, are printed on each array. The spacing therefore will be the size of a sub-array.

"topbottom" is the same as "subarrays" when there are two sub-arrays.

Value

Integer giving spacing between replicate spots in the gene list.

Author(s)

Gordon Smyth

See Also

An overview of LIMMA functions for reading data is given in 03.ReadingData.

Examples

getSpacing("columns",list(ngrid.r=2,ngrid.c=2,nspot.r=20,nspot.c=19))
getSpacing("rows",list(ngrid.r=2,ngrid.c=2,nspot.r=20,nspot.c=19))
getSpacing("topbottom",list(ngrid.r=2,ngrid.c=2,nspot.r=20,nspot.c=19))
[Package limma version 3.34.5 Index]