I'm currently working on a microarray dataset from NIH's Gene Expression Omnibus using R.
I was wondering how to plot a log intensity/density plot on a set of .CEL files that have been normalized.
I have been trying to following the example at this website: http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/
However, I am having creating a proper phenotype.txt file.
When I attempt to remove the phenotype.txt from the ReadAffy() command, I receive the following error when I run the gcrma function:
Computing affinities. Error in matrix(NA, nrow = max(cbind(pmIndex, mmIndex)), ncol = 1) : invalid 'nrow' value (too large or NA)
Is there an eassier way to download a set of .CEL files from GEO, normalize the microarray data, and then proceed to plot the log intensities?