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 > 2650 Crescent Drive, Suite 100 > Lafayette, CO 80026 > Direct: (303) 604-3265 > tyler.reed at thermofisher.com<mailto:tyler.reed at="" thermofisher.com=""> > www.thermoscientific.com/gen<http: www.thermoscientific.com="" gen=""> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

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 > > Thermo Fisher Scientific > 2650 Crescent Drive, Suite 100 > Lafayette, CO 80026 > Direct: (303) 604-3265 > tyler.reed at thermofisher.com<mailto:tyler.reed at="" thermofisher.com=""> > www.thermoscientific.com/gen<http: www.thermoscientific.com="" gen=""> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor