[BioC] arrayQualityMetrics for Agilent one color data

[James W. MacDonald]

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

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

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

Best,

Jim


>
> Thanks in advance!
>
> Yong
>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099