R: Extract the Print Layout of an Array from the GAL File

getLayout {limma}

R Documentation

Extract the Print Layout of an Array from the GAL File

Description

From the Block, Row and Column information in a genelist, determine the number of grid rows and columns on the array and the number of spot rows and columns within each grid.

Usage

getLayout(gal, guessdups=FALSE)
getLayout2(galfile)
getDupSpacing(ID)

Arguments

`gal`	data.frame containing the GAL, i.e., giving the position and gene identifier of each spot
`galfile`	name or path of GAL file
`guessdups`	logical, if `TRUE` then try to determine number and spacing of duplicate spots, i.e., within-array replicates
`ID`	vector or factor of gene IDs

Details

A GenePix Array List (GAL) file is a list of genes and associated information produced by an Axon microarray scanner. The function getLayout determines the print layout from a data frame created from a GAL file or gene list. The data.frame must contain columns Block, Column and Row. (The number of tip columns is assumed to be either one or four.)

On some arrays, each probe may be duplicated a number of times (ndups) at regular intervals (spacing) in the GAL file. getDupSpacing determines valid values for ndups and spacing from a vector of IDs. If guessdups=TRUE, then getLayout calls getDupSpacing.

The function getLayout2 attempts to determine the print layout from the header information of an actual GAL file.

Value

A printlayout object, which is a list with the following components. The last two components are present only if guessdups=TRUE.

`ngrid.r`	integer, number of grid rows on the arrays
`ngrid.c`	integer, number of grid columns on the arrays
`nspot.r`	integer, number of rows of spots in each grid
`nspot.c`	integer, number of columns of spots in each grid
`ndups`	integer, number of times each probe is printed on the array
`spacing`	integer, spacing between multiple printings of each probe

Author(s)

Gordon Smyth and James Wettenhall

Examples

# gal <- readGAL()
# layout <- getLayout(gal)

[Package limma version 3.34.5 Index]