search for: r_biocondmanu

...d of clusters. So, I was hoping if anyone could point me to a direction as to how to take advantage of the initial dendrogram and focus on specific clusters from which to derive the sub-clusters at a new given cutoff height. I recently found in this page http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual the following code: clid <- c(1,2) ysub <- y[names(mycl[mycl%in%clid]),] hrsub <- hclust(as.dist(1-cor(t(ysub), method="pearson")), method="complete") # Select sub-cluster number (here: clid=c(1,2)) and gene...

...t;http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/overLapper.R") I can generate the heatmap graphic. I just can't sort my columns without getting an error. The instructions I'm following are from the Bioconductor manual here: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_graphics_heat The specific section of instructions I'm using is this: ? Presence-Absence Matrices: to indentify memberships of items across large numbers of sample sets source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/overLapper.R") # Imports the require...

hello folks, i am learning R and microarray analysis from scratch using different sites. today i am doing an exercise from http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_functions the section i am at is 2. Affymetrix data analysis. I understand the syntax given in this section up until: design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) # Creates appropriate design matrix. Alternatively, such a design matrix can be created in any spreadsheet program an...