Hi all: I have 11 Human Genome U133 plus 2.0 samples. There are 2 of them are identity samples. I try to use correlation of samples to verify them. But even not identity samples have high correlations. here is my test code #read all 11 samples expression value table , (using MAS5) sample <- read.table("samples.txt",sep="\t") corelation <- cor(sample,sample,method="pearson") Could any one have any other ways to verify identity samples ? Sincerely, Chang Bang

จน@yzu wrote: > Hi all: > I have 11 Human Genome U133 plus 2.0 samples. > There are 2 of them are identity samples. > I try to use correlation of samples to verify them. > But even not identity samples have high correlations. > > here is my test code > #read all 11 samples expression value table , (using MAS5) > sample <- read.table("samples.txt",sep="\t") > corelation <- cor(sample,sample,method="pearson") > > Could any one have any other ways to verify identity samples ? I don't think correlation is a good measure here, primarily since you have so many observations per sample. Since noise is such a large component of the signal for many of the genes in a given sample, I find that correlation is higher than one might expect for samples that are unrelated, and lower than expected for samples that should be very similar. You might be better off using PCA and plotting the first two (or three) principal components. I find this to be a better 'eyeballometric' measure of similarity. See ?prcomp. Also note that you have to transpose your data because prcomp expects samples in rows and observations in columns, unlike the usual microarray paradigm. Best, Jim > > Sincerely, > Chang Bang > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623