addXYfromGAL {arrayQualityMetrics} | R Documentation

## Computing the coordinates of the spots on a slide

### Description

From the coordinates of the blocks of a microarray slide and the Row and Column locations of the spots within the blocks, `addXYfromGAL` computes the X and Y coordinates of the spots of a slide.

### Usage

    addXYfromGAL(x, gal.file, nBlocks, skip, ...)

### Arguments

`x` | is an `AnnotatedDataFrame` representing the featureData of an object.
`gal.file` | name of the file .gal that contains the coordinates of the blocks.
`nBlocks` | number of blocks on the slide.
`skip` | number of header lines to skip when reading the gal.file.
`...` | Arguments that get passed on to `read.table`.

### Value

The object `x` of class `AnnotatedDataFrame` will be returned with two added columns: X and Y corresponding to the absolute position of the probes on the array.

### Author(s)

Audrey Kauffmann, Wolfgang Huber. Maintainer: <audrey@ebi.ac.uk>

[Package arrayQualityMetrics version 1.2.1 Index]