Hi Lukas, thank you for your answer and the quick changes!
Regarding the MEDIPS.plotCalibrationPlot() function, I had actually rewritten the function to accept a "main" argument. Sorry, I forgot to mention that! I think the problem is indeed calling the png function before the loop. I usually use only pdf plots with multiple pages in order to avoid getting hundreds of separate files, so I forgot that doing the same with png() will not work out. Best regards, Nora > Message: 1 > Date: Mon, 25 Oct 2010 12:17:28 +0200 > From: Lukas Chavez Wurm <[email protected]> > To: [email protected] > Subject: Re: [Bioc-sig-seq] error with MEDIPS.CpGenrich -> resize +, > segfault in MEDIPS.plotCalibrationPlot > Hello, > > as recommended by Steve, the best is to switch to R 2.12. and to install > MEDIPS via biocLite(). > > However, your MEDIPS.CpGenrich(data=barr, extend=fraglen) induced error > will remain. This is because the resize() function has no start > parameter anymore. Therefore, we have updated our MEDIPS.CpGenrich() > function. The updated version (MEDIPS v. 1.1.2) should be available the > next days via biocLite(). Until then you can run the MEDIPS.CpGenrich() > function without specifying the extend parameter. By this, the CpG > density of your short reads will be tested without an additional > smoothing. This should be fine also. > > Regarding the error that appears in the context of the > MEDIPS.plotCalibrationPlot() function, I have seen that you try to > specify a main parameter that does not exist. I have also updated the > MEDIPS.plotCalibrationPlot() function in order to allow defining custom > headers for the plots by a main parameter (also available from version > 1.1.2). Until then try to create the calibration plots without > specifying a main parameter. I have also seen that you first call the > png() function and afterwards calibration plots are plotted in a loop. > Maybe you can try to create the calibration plots one after the other in > the loop as: > > for(bar in calib_list){ > png(paste("Calibration_plot_bar", counter, ".png", sep="")) > MEDIPS.plotCalibrationPlot(data=bar, linearFit=T, plot_chr="all", rpm=T, > xrange=10) > dev.off() > counter=counter+1 > } > > All the best, > Lukas >
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