Hi Dario,

Thanks for those corrections. I now have the graph made. However, I'd like to modify the main title for the plot, the axis labels and the legend. I tried using xlab,ylab etc. to set the labels for the axes but get an error. Is there a way that I can do this?

Pankaj



On Saturday, November 23, 2013 3:00 AM, Dario Strbenac <dstr7320@uni.sydney.edu.au> wrote:
 
It turns out that the problems were that the some of the variables were in the wrong format.
 
Firstly, p.anno isn't being handled by the code correctly if it doesn't have an index column. The documentation says index is optional. Do probes$index <- 1:nrow(probes) before giving probes to featureScores. You'll also want to set log2.adj = FALSE for your type of data. Otherwise, zero methylation becomes negative infinity. Secondly, the ordering data frame expects numeric or factor type columns. You provided integer. Thirdly, the length of your ordering was the same as the number of probes, rather than the number of genes. The  correct code for the ordering parameter is data.frame(factor(rep(1, nrow(genes)))).
 
I will add more error checking code for the user inputs to the next version and ensure featureScores works when there isn't an index column for p.anno.
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