[BioC] Drosophila tiling array background correction

Benjamin Lansdell lansdell at wehi.EDU.AU
Wed Jul 16 02:53:03 CEST 2008


I have been trying to analyse drosophila development tiling arrays  
using Bioconductor. In particular I would like to perform some form  
of background correction for probe affinities (such as GCRMA) and  
then quantile normalisation but have been unable to find any packages  
that can do so without a .cdf file. I have a collection of .cel files  
and a .bpmap file.

I know the package oligo can perform RMA using a package that you  
build from a .bpmap file but this isn't quite what I want.

Is it possible to create the necessary structures myself (AffyBatch,  
something that contains the probe sequences, etc) for use with the  
many packages that seem to rely on a .cdf file?

Thanks in advance,

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