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>
> 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
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