Using Geneplotter R package, there is a function named plotMA (http://www.bioconductor.org/packages/2.13/bioc/manuals/geneplotter/man/geneplotter.pdf). To get the plot, your object (data.frame) needs at least three columns, the first containing the mean expression values (for the x-axis), the second one is logarithmic fold change (for the-y axis) and the third is a logical vector indicating significance (for the coloring of the dots). I have attached my file. I uploaded the file via Rcmdr with the name of my data-set as dat1 and then input the following command:
plotMA(dat1, ylim = NULL, colNonSig = "gray32", colSig = "red3", colLine = "#ff000080", log = "x", cex=0.45, xlab="mean expression", ylab="log fold change")
However, it gave me the following error:
Error in .local(object, ...) :
When called with a data.frame, plotMA expects the data frame to have 3 columns, two numeric ones for mean and log fold change, and a logical one for significance.
I tried many things, without any luck. Any suggestions?
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