[BioC] within chip probe replicates, Agilent chips

[Peter Langfelder]

Hello,

the package WGCNA contains the function collapseRows that uses simple
statistical approaches to summarize different (or duplicate) probes
for the same gene. The method is described here:

Miller JA, Cai C, Langfelder P, Geschwind DH, Kurian SM, Salomon DR,
Horvath S (2011) Strategies for aggregating gene expression data: The
collapseRows R function. BMC Bioinformatics12:322. PMID: 21816037,
PMCID: PMC3166942

The web page for data and R code from the article is

http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/collapseRows/

HTH,

Peter

On Mon, Oct 29, 2012 at 4:33 PM, Reed, Tyler
<tyler.reed at thermofisher.com> 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
>
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