[BioC] arrayQualityMetrics for Agilent one color data

James W. MacDonald jmacdon at uw.edu
Tue Dec 3 16:23:42 CET 2013

Hi Yong,

On Tuesday, December 03, 2013 4:56:11 AM, Yong Li wrote:
> Dear list members,
> I have an expression array dataset done with Agilent one color array, and I
> wanted to do QC using arrayQualityMetrics. I read in the raw Agilent data
> using limma and background correct and normalization was done according to
> limma User's guide. This works fine and I got an EList object. However it
> seems arrayQualityMetrics doesn't accept EList as input. Any one has an
> idea?

Your best bet is probably converting the EList object into an 
ExpressionSet. The simplest way to do so is something like

eset <- ExpressionSet(assayData = assayDataNew(exprs = EList$E))

but you can always add in the other slots (phenoData, featureData, etc) 
if you so desire.



> Thanks in advance!
> Yong
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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