xy2indices {affy}R Documentation

Functions to convert indices to x/y (and reverse)

Description

Functions to convert indices to x/y (and reverse)

Usage

xy2indices(x, y, nr = NULL, cel = NULL, abatch = NULL)
indices2xy(i, nr = NULL, cel = NULL, abatch = NULL)

Arguments

x X position for the probes
y Y position for the probes
i indices in the AffyBatch for the probes
nr total number of Xs on the chip
cel a corresponding object of class Cel
abatch a corresponding object of class AffyBatch

Details

The probes intensities for given probe set ids are extracted from an AffyBatch object using the indices stored in the corresponding cdfenv.

Value

A vector of indices or a two-columns matrix of Xs and Ys.

Author(s)

L.

See Also

indexProbes

Examples

data(affybatch.example)

pm.i <- indexProbes(affybatch.example, which="pm", genenames="AFFX-BioC-5_at")[[1]]
mm.i <- indexProbes(affybatch.example, which="mm", genenames="AFFX-BioC-5_at")[[1]]

pm.i.xy <- indices2xy(pm.i, abatch = affybatch.example)
mm.i.xy <- indices2xy(mm.i, abatch = affybatch.example)

image(affybatch.example[1], transfo=log2)
## plot the pm in red
plotLocation(pm.i.xy, col="red")
plotLocation(mm.i.xy, col="blue")


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