[BioC] normalizeByReference package for Affymetrix ChIP-chip data

Wolfgang Huber huber at ebi.ac.uk
Tue May 26 23:53:56 CEST 2009

Dear Jennifer

I assume you mean the normalizeByReference function in the tilingArray 

1. the "background" parameter refers to probes on the array, not 
samples. Here, you need to specify an (as large as possible) set of 
probes for which you expect no enrichment signal. These are used to 
estimate the typical background signal also for all other probes by 

2. You don't need a probeAnno object to call this function, so I am not 
sure why you are asking?

Please let me know if you have any questions that are not well answered 
by the manual page of this function.

Best wishes

Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber

JENNIFER JUDY ha scritto:
> Hello.
> We are currently trying to apply the normalizeByReference package to Affymetrix ChIP-chip data for human and mouse samples. Specifically, I am looking for advice regarding the background parameters (are control samples sufficient in this case). Additionally, does anyone have advice on how to create a probeAnno object with Affy's bpmap files? 
> Any help is much appreciated!
> Thanks,
> Jen
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