On Mon, Dec 6, 2010 at 6:00 PM, Wei Shi <shi@wehi.edu.au> wrote:

> Dear Viritha:
>
>        I think you can normalize the gProcessed signal directly.
>
>        Also there are ~100 negative control genes on this microarray
> platform which might be useful for the background correction and
> normalization. The nec() function in limma can use these negative controls
> to perform a normexp background correction. After that, you will normalize
> your data using cyclic loess method or the quantile method.
>
>
Hi, Wei.

I may be mistaken, but I think the gProcessedSignal is already 2D-loess
background-corrected by the Agilent FE software.

Sean


>        Hope this helps.
>
>
> Cheers,
> Wei
>
> On Dec 7, 2010, at 9:47 AM, Martin Morgan wrote:
>
> > On 12/06/2010 01:44 PM, viritha kaza wrote:
> >> Hi Group,
> >> I am interested in performing normalization with the agilent data
> >> -Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature
> >> Number version).The gProcessed signal has been deposited as a series
> >> matrix file in Geo. I wanted to know if one can directly normalize
> >> gProcossed signal or need any other parameters from feature extraction
> >> file before one can perform cyclic loess normalization?
> >> Thank you in advance,
> >> Viritha
> >
> > Please ask on the Bioconductor mailing list
> >
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
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