"paul murima" <[EMAIL PROTECTED]> writes: > Hello R-Community, > > I am a rookie in R and I am fascinated with the power of bio computing > by R. I am analysing gene expression data from Real time PCR. I have > used absolute gene quantitation to measure gene copy number in all my > transcripts. All my data has been normalised them to a housekeeping > gene, which is constitutive expressed. > > My problem is as follows. > After normalising some of the genes (which are feature vectors in my > matrix of 26 treatment conditions) are up regulated to over 50 fold.
Do you know about http://bioconductor.org ? Reviewing their mailing list archives and asking on their mailing list will likely lead to a number of informed opinions about normalization. Martin > Now, when plot my heatmap.2 of the matrix, almost everything shows up > as red, in a green-red colour scale. > i.e. from -1,0,1. Is there a way to scale all the data on the matrix > such that when i plot it on a heat map it it reflecting the relative > expression of of each feature, against the treatment condition without > being fixed to the -1, to 1 scale. > Below is how the code i used. > > library(gplots) > zcz<- read.table("chitekete.csv", header = T, row.names=1, sep=","); > xcc <- cor(zcz); > pdf("SIGA.pdf", height=10,width=9) > heatmap.2(xcc, margins= c(9,9), col = bluered(64), trace=c("none"), > breaks=c(seq(-1,1,1/32)), symkey=TRUE, density.info="histogram", > cexRow=1) > > I thank you all. > > Paul > > > > -- > BEST > > Paul Murima > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
