How to create microarray pictures

Go to parent Analyze your own microarray data in R/Bioconductor

The code on this page works for both affy and oligo

How to print the raw intensities of each array ?

For each array we will generate a figure containing the image of that array. You see that the sample names that you specified in the phenoData are indeed used as labels in the figure for (i in 1:6) { name = paste("image",i,".jpg",sep="") jpeg(name) image(data[,i],main=ph@data$sample[i]) dev.off() } This code was used to analyze an experiment containing 6 arrays. If you have a different number of samples you have to adjust the numbers in the code, e.g. if you have 8 arrays: for (i in 1:8) { name = paste("image",i,".jpg",sep="") jpeg(name) image(data[,i],main=ph@data$sample[i]) dev.off() }

The figure below shows all microarray images on the same figure. This works for small arrays but gives problems for human arrays since they are so big that it's hard to fit them on a single figure. That's why the code above generates a separate figure for each array.

However, if you have a set of 6 small arrays (like the ATH arrays) and you want to plot them on a single plot, you can use the following code for the plotting:

op = par(mfrow = c(2,3))
for (i in 1:6){image(data[,i],main=ph@data$sample[i])}

par(mfrow = c(2,3)) defines that you want to plot the 6 figures in a grid of 2 rows and 3 columns.

So if you have 3 groups of 3 replicates and you want to plot them on a single plot, the code becomes:

op = par(mfrow = c(3,3))
for (i in 1:9){image(data[,i],main=ph@data$sample[i])}