Hi Bioconductor, i am new to the Bioconductor world and have a question i hope you can help me with. I wish to compute the pearson correlation of the expression values between a gene of interest and a number of other genes in a number of experiments. Can someone direct me to the relevant Bioconductor package ? Thankyou Rick ____________________________________ Dr. Richard Dixon Dept. of Cardiovascular Sciences, University of Leicester, Clinical Sciences Wing, Glenfield Hospital, Leicester, LE3 9QP UK Tel: (0116) 250 2541 Fax: (0116) 287 5792 e-mail: rd67@le.ac.uk

Hi Rick, You could use the function cor to compute these correlations. Check out: ?cor Cheers, Steffen Dixon, Dr R. wrote: >Hi Bioconductor, > >i am new to the Bioconductor world and have a question i hope you can help me with. >I wish to compute the pearson correlation of the expression values between a gene of interest and a number of other genes in a number of experiments. > >Can someone direct me to the relevant Bioconductor package ? > >Thankyou >Rick >____________________________________ > >Dr. Richard Dixon > >Dept. of Cardiovascular Sciences, >University of Leicester, >Clinical Sciences Wing, >Glenfield Hospital, >Leicester, LE3 9QP >UK > >Tel: (0116) 250 2541 >Fax: (0116) 287 5792 >e-mail: rd67@le.ac.uk > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > >

Hi Rick Have you tried looking at cor() with method="pearson"? I guess that should do the trick. Just type ? cor for more info. It's from the basic 'stats' package. If you don't have too many genes, you can also plot the correlations using for example plot.cor() from the 'sma' package. HTH \Heidi On Mon, 26 Jul 2004, Dixon, Dr R. wrote: > Hi Bioconductor, > > i am new to the Bioconductor world and have a question i hope you can help me with. > I wish to compute the pearson correlation of the expression values between a gene of interest and a number of other genes in a number of experiments. > > Can someone direct me to the relevant Bioconductor package ? > > Thankyou > Rick > ____________________________________ > > Dr. Richard Dixon > > Dept. of Cardiovascular Sciences, > University of Leicester, > Clinical Sciences Wing, > Glenfield Hospital, > Leicester, LE3 9QP > UK > > Tel: (0116) 250 2541 > Fax: (0116) 287 5792 > e-mail: rd67@le.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Dixon, Dr R. wrote: > Hi Bioconductor, > > i am new to the Bioconductor world and have a question i hope you can help me with. > I wish to compute the pearson correlation of the expression values between a gene of interest and a number of other genes in a number of experiments. > > Can someone direct me to the relevant Bioconductor package ? R base is enough to do so, however the data structures in Biobase are convenient to handle your data: library(Biobase) data(eset) got <- "AFFX-MurIL2_at" # Gene Of inTerest mycor <- apply(exprs(eset), 1, cor, y=exprs(eset)[got, ]) L. > Thankyou > Rick > ____________________________________ > > Dr. Richard Dixon > > Dept. of Cardiovascular Sciences, > University of Leicester, > Clinical Sciences Wing, > Glenfield Hospital, > Leicester, LE3 9QP > UK > > Tel: (0116) 250 2541 > Fax: (0116) 287 5792 > e-mail: rd67@le.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >