Hi Wolfgang, Thank you for your help. Please forgive me always asking some naive questions as I have never used the R language before and I have to learn everything from zero. My question is how I can show the correlation with ?pearson? instead of "spearman" in the HTML reports. My understanding is when I call repAgree <- getMeasureRepAgreement(xn, corr.method = "pearson"), the results are stored in the asssayData slot of the cellHTS2 object. Then how can I let it show in the reports? Thank you so much! Ning sessionInfo() cellHTS2 R version 2.11.1(2010-05-31)

Dear Ning Try typing library("cellHTS2") ? getMeasureRepAgreement into the R interpreter. You'll get: Value: The function generates a list with elements: "repStDev": matrix with the calculated repeatability standard deviation between plate replicates. It has dimensions 'nrPlates x nrChannels'; "corrCoef" (if the number of replicates equals 2): matrix with the correlation coefficients between plate replicates. It has dimensions: 'nrPlates x nrChannels'; "corrCoef.min" (if the number of replicates is greater than 2): matrix with the minimum value of the correlation coefficients between plate replicates. It has dimensions 'nrPlates x nrChannels'; "corrCoef.max" (if the number of replicates is greater than 2): matrix with the maximum value of the correlation coefficients between plate replicates. It has dimensions 'nrPlates x nrChannels'. Does this answer your question? Best wishes Wolfgang On 13/08/10 17:47, Ning wrote: > Hi Wolfgang, > > Thank you for your help. Please forgive me always asking some naive questions as > I have never used the R language before and I have to learn everything from zero. > > My question is how I can show the correlation with ?pearson? instead of > "spearman" in the HTML reports. > > My understanding is when I call > > repAgree<- getMeasureRepAgreement(xn, corr.method = "pearson"), > > the results are stored in the asssayData slot of the cellHTS2 object. > > Then how can I let it show in the reports? > > Thank you so much! > > Ning > > sessionInfo() > > cellHTS2 > R version 2.11.1(2010-05-31) > > _______________________________________________ > 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