Hi I am following the 'Single channel analysis of Agilent microarray data with Limma' given at http://matticklab.com/index.php?title=Single_chan nel_analysis_of_Agilent_microarray_data_with_Limma. >From starting with the shortened code given at the top of the webpage, I have been able to produce boxplots and MA plots for the prenormalized and normalized data, and volcano plots for the normalized data. I'm able to export the pre-normalized and normalized data, and have generated output files (from topTable) for the various coefficients I am testing. However, I'm having problems creating imageplots from the data. I've had a look at the script given at https://stat.ethz.ch/pipermail/bioconductor/2007-January/015532.html and have tried various ways of modifying it to get it to work for my data. Please find below an excerpt of my script. The output I get when the script gets to the imageplot part of this version of the script is 'Error in (row - 1) * nc + c : non-numeric argument to binary operator'. I am not sure where I am going wrong. Any help as to how to correct the code would be greatly appreciated. Thanks Lesley ------------------------------------------- targets <- readTargets("Targets.txt") x <- read.maimages(targets, path="assays/", source="agilent.median",green.only=TRUE) #x = $E, $Eb, $targets, $genes, $source ##Create boxplot of pre-normalized data png("QC/Raw_data/Boxplot_prenormalization.png")' boxplot(log2(x$E) ~ col(x$E), names = targets$Patient_id, las = 2, ylab = "E", main = "Pre-normalized data") dev.off() ##Produce pseudo-MA plots for pre-normalized data E <- log2(x$E) #Log2 transform the values A <- matrix(rowMeans(E),nrow(E),ncol(E)) MA <- new("MAList",list(M=E,A=A)) png("*.png") plotMA3by2(MA) #Can use plotMA3by2() for single channel data by making a pseudo two-color data object dev.off() ##read.maimages() doesn't set the $printer information automatically for Agilent data; need to expand out the data vector to be the right length by adding NAs in the right places, so that imageplot() can be used https://stat.ethz.ch/pipermail/bioconductor/2007-January/015532.html r <- x$genes$Row c <- x$genes$Col nr <- max(r) nc <- max(c) y <- rep(NA,nr*nc) i <- (r-1)*nc+c y[i] <- log2(x$E) imageplot(y,x$printer) -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.12.1 -- Sent via the guest posting facility at bioconductor.org.