G'day, I think you probably have an R configuration issue. Could you please share your .BAT file please.
Also add the following lines to your .BAT file directly after the line that sets JRI_LIB_PATH: rem Some debug. set dir "%R_HOME%" dir "%R_HOME%\bin\x64" dir "%JRI_LIB_PATH%" This will provide some debug. Then run MZmine and send us the output to the Command console when MZmine first starts up. It should include your environment variables and directory listings. Then please try baseline correction and send us the error message it produces in the Command console. Finally, please run R and tell use the output of the following command: .libPaths() As for your second question about m/z tolerances and noise parameters I'll defer to other members of the list as it's not my area of expertise. Regards, Chris. On 02/05/12 11:45, YS LING wrote: > G'day Chris, > > Sorry for late reply as i dig this mail from the junk mail box (for > some reason it went there). > Yes, I had installed the R as you told me and i had set all the > parameters. Yet the baseline correction still has the problem when i > tried to run baseline correction, the MZmine window just shut down. > > And one more thing, since i'm using Thermo QqQ to collect my data > under parent ion scan mode, do u mind to tell me what's the parameter > range for example, the mass tolerance (either m/z or ppm) or the noise > signal. It is a bit complicate and i'm a new user to MZmine. I believe > the default parameters are subjected to QTOF since Dr Oresic research > group mainly used mainly QTOF for their research. > > Or may be you can tell me how purpose of each of these parameters > since not much details been written on MZmine manual. > > Thank you very much. > > 2012/4/24 Pudney Chris (ext) GBJH <chris.pud...@syngenta.com > <mailto:chris.pud...@syngenta.com>> > > G'day, > > I've been on leave so have only just come across the thread > regarding baseline-correction problems. > > Yee-Soon did you manage to resolve this issue? > > The error message you showed indicates that you haven't customised > the start-up script file correctly (startMZmine_Windows.bat). > > Getting baseline correction working is fiddly. Here's what you > need to do: > > 1. Install R > 2. In R install the rJava package: install.packages("rJava") > 3. In R install the ptw package: install.packages("ptw") > 4. Configure your startMZmine_Windows.bat file. The one we use for > Windows 7 (64-bit) and R 2.15 is attached (rename the extension > to .BAT) > > You will need to customise the following: > > set R_HOME=... > > This is the R home directory. It should contain the bin, include, > doc and share sub-directories. > > set PATH=%PATH%;.. > > This is the search path variable. Append (semi-colon separator) > the directory that contains the R executables (R.exe, Rcmd.exe, > ...) and libraries (R.dll, Rblas.dll, ...) > > set R_LIBS_USER=... > > This is the directory where R packages are installed. It should > contain the rJava and ptw sub-directories. It should be listed > when you run the .libPaths() command in R. > > set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri > > This the the directory holding the JRI library (JRI.dll). It > should be a sub-directory of R_LIBS_USER. In some cases both an > i386 and x64 sub-directory are present each containing a different > JRI.dll. Choose the sub-directory appropriate for your > architecture, i.e. 32-bit choose i386, 64-bit choose x64. > > Regards, > Chris. > > > > > This message may contain confidential information. If you are not > the designated recipient, please notify the sender immediately, > and delete the original and any copies. Any use of the message by > you is prohibited. > > > > > -- > Yee-Soon LING This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
