Peter, have a look at the section on variance stabilising transformation of the count data in DESeq's vignette. After that, as Naomi says, you can simply use "cor". Calling "cor" directly on the count data might not be overly useful, because of the heteroskedasticity and skewness of the count data, such that the correlation coefficients would likely be dominated by few extreme data points. Best wishes Wolfgang On Jul/30/10 3:59 AM, Naomi Altman wrote: > This is easily done without DESeq. E.g. you could use the cor function > to compute correlations, and pairs to plot all pairs of samples. > > --Naomi > > At 06:42 PM 7/28/2010, Pete Shepard wrote: >> Hi All, >> >> I am wondering if the DESeq package for Bioconductor has a function to >> plot >> and calculate the Pearson correlation for biological replicates? >> >> TIA >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber