Tim Triche, Jr. <tim.triche at="" ...=""> writes: > > try qc.probe.plot() > I tried using qc.probe.plot. I have methylumi version 2.0.13 ( from Bioconductor version 2.9) I installed ggplot2_0.9.0. I also had to install the reshape package. However, when I ran the qc.probe.plot function (e.g. qc.probe.plot(lumi450k, "NORM_A")), I got the following error: Error in qc.probe.plot(lumi450kData, controlTypes(lumi450kData)[1]) : could not find function "scale_x_log2" I looked at the functions available in the ggplot2 package, and I saw that while there was no "scale_x_log2" function, there was a scale_x_sqrt and a scale_y_sqrt function. While I accept that log2 and square root aren't equivalent, I downloaded the sourcecode for the file that contains qc.probe.plot, changed the function calls for "scale_x_log2" and "scale_y_log2" to "scale_x_sqrt" and "scale_y_sqrt" respectively. The qc.probe.plot function now worked. It also worked when I used "scale_x_log10" and "scale_y_log10". My question is: what versions of methylumi and ggplot do I need to be using, in order to get the qc.probe.plot function to work, without modifying the qc.probe.plot function? Is there a version of ggplot which contains the scale_x_log2/scale_y_log2 functions? Cheers, Olly

I need to patch this to detect what version of ggplot2 is installed and choose the appropriate execution path. You can use ggplot 0.89 for now, but that's obviously not satisfactory behavior over the long term. The scaling functions have been moved into the 'scales' package; I need to find out how to replace the ggplot2 0.89-and-earlier behavior for this. Will post as soon as I have implemented it and will send a pull request to incorporate it into devel and stable releases. There are some other warnings that I need to mop up (i.e. that are my fault) as well. Thank you for reminding me, --t On Mon, Mar 19, 2012 at 7:33 AM, Oliver Lyttleton <o.lyttleton@bristol.ac.uk> wrote: > > > Tim Triche, Jr. <tim.triche@...> writes: > > > > > try qc.probe.plot() > > > > I tried using qc.probe.plot. > > I have methylumi version 2.0.13 ( from Bioconductor version 2.9) > > I installed ggplot2_0.9.0. > > I also had to install the reshape package. > > However, when I ran the qc.probe.plot function (e.g. > qc.probe.plot(lumi450k, > "NORM_A")), I got the following error: > > Error in qc.probe.plot(lumi450kData, controlTypes(lumi450kData)[1]) : > could not find function "scale_x_log2" > > I looked at the functions available in the ggplot2 package, and I saw that > while > there was no "scale_x_log2" function, there was a scale_x_sqrt and a > scale_y_sqrt function. While I accept that log2 and square root aren't > equivalent, I downloaded the sourcecode for the file that contains > qc.probe.plot, changed the function calls for "scale_x_log2" and > "scale_y_log2" > to "scale_x_sqrt" and "scale_y_sqrt" respectively. > > The qc.probe.plot function now worked. It also worked when I used > "scale_x_log10" and "scale_y_log10". > > My question is: what versions of methylumi and ggplot do I need to be > using, in > order to get the qc.probe.plot function to work, without modifying the > qc.probe.plot function? Is there a version of ggplot which contains the > scale_x_log2/scale_y_log2 functions? > > Cheers, > > Olly > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]