Dear Tomas,
Thank you very much for a quick response. here, I am sending you the data
files.
I have uploaded the file in google drive and shared the file. I hope you
will be able to look at this.
https://drive.google.com/folderview?id=0Bz183RKCUevxRW9EdmVhejZIaDQ&usp=sharing
Since, I am new to this software and already sending you the data files,
may I also take this opportunity to ask you further about the parameters? I
am closely looking at the peak 166.02, which is phenylalanine (monoisotopic
mass: 165.07898). With the parameters i gave (attached along with data)
leads to two separate peaks during peak alignment. Since this is a
reference sample, i am not expecting two peaks at 4 min. is it possible
that I have to relax m/z and/or RT tolerance during processing?
Thank you and apologize for taking your time.
jam
On Fri, Feb 6, 2015 at 12:26 AM, Tomas Pluskal <plus...@oist.jp> wrote:
> Hi Jamuna,
>
> I think you don’t need to worry about the R warnings in the console.
> These should be harmless.
>
> However, I notice the TIC visualizer shows a strange line in the
> chromatogram plot of your data. Could you perhaps send us a sample data
> file, so we can debug this problem?
>
> Tomas
>
>
>
> On Feb 6, 2015, at 04:01, jamuna risal <jri...@gmail.com> wrote:
>
> I am running MzMine 2.12 in 64 bit Win OS. java version 8 and R-3.1.2 in
> 64 bit.
> I have not changed heap size but slightly adjusted the R_Home
> in startMzMine script.
>
> I converted .RAW data to MzXML format using msConvert of the
> proteoWizard. After importing raw file, I did crop filter and then started
> the baseline correction using peakdetection baseline corrector (Parameters:
> TIC, m/z bin width of 0.5 and no. of scans left and right 20, and lwin and
> rwin 5 and multiplier 1). There is a R- error message, however, at the end
> it says baseline corrected and I can see that in the chromatogram also.
>
> If somebody can suggest me what is the error and what is it doing or not
> doing for the baseline correction, I would really appreciate the response.
>
> Thanks.
>
> jam
>
>
>
> --
> Jamuna Risal Paudel
> <Baseline.PNG><command.PNG>
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> ===============================================
> Tomas Pluskal
> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
> University
> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
> WWW: https://groups.oist.jp/g0
> TEL: +81-98-966-8684
> Fax: +81-98-966-2890
>
>
--
Jamuna Risal Paudel
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sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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