[BioC] How to use affy's image function on RMA values?

Malard, Joel M JM.Malard at pnl.gov
Thu Jun 9 03:47:14 CEST 2005


I would like to compare (visually) the raw intensities of 40 affymetrix
MOE430A arrays with the corresponding expression values computed by RMA,
e.g. using the function image.
It seemed  a good idea to replace the exprs component of the AffyBatch
object with the exprs component of the object returned by justRMA but
that does not work.

	data <- ReadAffy(filenames=c("A1.CEL", etc, "A40.CEL"));

	exprs(data) <- exprs(justRMA(filenames=c("A1.CEL", etc,

The error message is:

> image(data[,1]);
Warning message:
data length [22690] is not a sub-multiple or multiple of the number of
rows [712] in matrix

The resulting image shows diagonal lines that shouldn't be there.

Could anyone put me on the right track?

Thanks for your help.

Joel Malard

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