[BioC] Robustspline and two dimentional loess for two color agilent data

[Gordon K Smyth]

Dear Samaneh Fazeli,

I am guessing that this is question about

  normalizeWithinArrays(RG, method="robustspline")

in the limma package.  When there are no print tips, robust-spline 
normalization reduces to loess normalization.  Hence you should use:

  normalizeWithinArrays(RG, method="loess")

for Agilent arrays.

Best wishes
Gordon


> Date: Thu, 21 Aug 2014 01:54:20 -0700 (PDT)
> From: "Samane [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, samanefazeli at gmail.com
> Subject: [BioC] Robustspline and two dimentional loess for two color
> 	agilent	data
>
> Hi

> Since there is no print tip in Agilent technology, Could I use 
> robust-spline and two dimensional loess on such data sets? I am 
> comparing some normalization methods on two color Agilent data; In the 
> most of times, robust-spline goes the best method based on comparison of 
> variance and ICC among replicated arrays. However I can not find lots of 
> papers which have applied these methods on Agilent data.

> I am looking forward to hearing from u.
> Regards,
> Samaneh Fazeli
>
>
> -- output of sessionInfo():
>
> R
>
> --
> Sent via the guest posting facility at bioconductor.org.

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