[BioC] within chip probe replicates, Agilent chips

[James W. MacDonald]

Hi Tyler,

You can use duplicateCorrelation(), as long as the replicates are 
regularly spaced. If you are using one of the 4X44 Agilent chips, the 
Agi4x44PreProcess package has some facilities for looking at the 
duplicate probes, but nothing to do e.g., mixed models with them.

Best,

Jim



On 10/29/2012 7:33 PM, Reed, Tyler wrote:
> Typically, how does one handle within-chip probe replicates on the Agilent microarray's to improve the significance of statistical tests?  I am currently using limma, and probes seems to be treated individually and only replicates across chips are considered in the statistical tests.
>
> Tyler Reed
> Associate Bioinformatics Developer
> Thermo Scientific Genomics
>
> Thermo Fisher Scientific
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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