Dear Barbara both are actually not very useful for this purpose (and, as Sean said, in about equal measure). For one alternative, have a look at the 'idr' package on CRAN and this paper: Q. Li, J. B. Brown, H. Huang and P. J. Bickel (2011). Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics. www.stat.berkeley.edu/tech-reports/790.pdf Best wishes Wolfgang Jul/23/12 4:17 PM, Sean Davis scripsit:: > On Mon, Jul 23, 2012 at 7:58 AM, Barbara Uszczynska <uszczynska at="" gmail.com="">wrote: > >> Dear Conductors, >> >> Is it better to use Pearson's or Spearman's correlation coefficient to >> measure the reproducibility among microarray biological replicates? >> >> I would be grateful for any hint. >> >> > Typically, after normalization, they will be nearly the same since the > effect of normalization is often to make the distributions of the arrays > similar. > > Sean > > [[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 > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber