Hi, I have an Agilent Dye Swap experiment, two colors, where I have my samples Resistant and Sensible
Distributed like this (this is my targets.txt file)
SampleNumber FileName Cy3 Cy5 1 A.txt S R 2 B.txt R S 3 C.txt S R 4 D.txt R S 5 E.txt S R 6 F.txt R S 7 B1.txt R S 8 C1.txt S R 9 D1.txt R S 10 E1.txt S R 11 F1.txt R S
I analyzed the data using the nex code
library(limma) targets <- readTargets("targets_all.txt") RG <- read.maimages(targets,source="agilent.median") RG <- backgroundCorrect(RG, method="normexp", offset=16) MA <- normalizeWithinArrays(RG, method="loess") MA.avg <- avereps(MA, ID=MA$genes$ProbeName) design <- modelMatrix(targets, ref="S") fit2 <- eBayes(fit) output <- topTable(fit2, adjust="fdr", coef="R", number=nrow(fit2), genelist=MA.avg$genes) genes_diff_expr.005<- subset(output,output$adj.P.Val < 0.05) pdf("heatmap_diff_exprs_R_S.pdf") heatmap.2(MA$M[rownames(MA$M) %in% genes_diff_expr.005$ProbeName,], trace="none", col=greenred(10),cexRow=0.2,labRow=NA,cexCol=0.7) dev.off()
Now, I want to see how my samples cluster for this signature. I've been doing so many heatmaps in years, mainly using Affymetrix or Agilent one color experiments, but I don't know how to use to plot all the samples distributed in the two channels (R). Using MA$M, I got the log2ratios, the point is that the name of my columns are as in targets A,B,C and so on, and I want R or S, but distributed in two channels I don't know how to specify which is sensible or resistant
any ideas?
Thanks in advance