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

### See Also

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

### Examples

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

[Package limma version 3.42.2 Index]