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
[email protected] wrote:
Date: Fri, 22 Oct 2010 09:48:53 -0400
From: Steve Lianoglou <[email protected]>
To: Nora Rieber <[email protected]>
Cc: "[email protected]"
<[email protected]>
Subject: Re: [Bioc-sig-seq] error with MEDIPS.CpGenrich -> resize +
segfault in MEDIPS.plotCalibrationPlot
Message-ID:
<[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
Hi Nora,
On Fri, Oct 22, 2010 at 9:17 AM, Nora Rieber
<[email protected]> wrote:
Dear all,
I am working with the MEDIPS package and get the following error when
calling the function MEDIPS.CpGenrich:
cpgEnrichment_barr<-MEDIPS.CpGenrich(data=barr,extend=fraglen)
Preprocessing...
Error in .local(x, width, fix, use.names, ...) :
unused argument(s) (start = FALSE)
Calls: MEDIPS.CpGenrich -> resize -> resize -> .local
I checked the resize function which indeed does not require a "start"
argument, the function call in MEDIPS.CpGenrich however looks like this:
ranges(pos2) <- resize(ranges(pos2), extend + 1, start = FALSE)
This sounds like a version problem.
This is my sessionInfo:
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
You're correct in thinking that it's a version problem and I'm pretty
sure that upgrading to the latest version of R (2.12) will solve your
problem.
It looks as if the MEDIP package was just released in bioconductor 2.7
(which is only meant to run on R 2.12), so I guess you installed MEDIP
by some "other" (not supported) means?
Keep in mind that using biocLite to install your packages is probably
the best way to ensure that you don't run into versioning problems, so
go ahead and:
(i) download/install the latest R;
(ii) biocLite() your way into the base bioconductor install; and
(iii) biocLite("MEDIP")
You should be good to go after that.
Hope that helps,
-steve
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