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

1
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: <kauffmann@bergonie.org>