[Bioc-sig-seq] error with MEDIPS.CpGenrich -> resize +, segfault in MEDIPS.plotCalibrationPlot

Nora Rieber n.rieber at dkfz-heidelberg.de
Tue Oct 26 14:17:00 CEST 2010

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,

> Message: 1
> Date: Mon, 25 Oct 2010 12:17:28 +0200
> From: Lukas Chavez Wurm <chavez at molgen.mpg.de>
> To: bioc-sig-sequencing at r-project.org
> 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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