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Topics - plasma33

1
XCMS / Peak List Generation
Hi Guys,

I want to generate a peak list with intensities in respect to the precursor ions so that I can do the MS/MS spectrum Match Analysis. I have got a result output file from metlin which are purely MS/MS. I did the mass search with help of the CAMERA Result and and filtered the ms2 data out of it. The masses in the output file are the precursor ions. I want the peak list and intensities generated by means of xcms so that I can search on Metlin - MS/MS Spectrum Match. I know that we can do by Xcalibur and Mass Frontier but I want to do via XCMS - R.

I am sending the link for Metlin Result File. Its modified but the content are same.
http://http://www.mediafire.com/?416td277ubu75hp

Thanks in advance guys.

Cheers
plasma33
2
XCMS / xcmsRaw Error
Hi guys,

I am getting an error which is [unable to find an inherited method for function "collect", for signature "xcmsRaw"]. Can anyone give me a fix for the suggested error.

Here is the code from R->
Code: [Select]
R version 2.14.2 (2012-02-29)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(xcms)
> xraw <- xcmsRaw("C:/Users/vnai039/Downloads/XCMS Results/Mutant Aux/Mutant-aux-1.mzXML", includeMSn=TRUE)
> xraw
An "xcmsRaw" object with 759 mass spectra

Time range: 0.4-2997.6 seconds (0-50 minutes)
Mass range: 121.0017-999.9907 m/z
Intensity range: 777.266-43677300

MSn data on  2113  mass(es)
        with  2322  MSn spectra
Profile method: bin
Profile step: 1 m/z (880 grid points from 121 to 1000 m/z)

Memory usage: 17.4 MB
> col<-collect(xraw, rt=20)
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "collect", for signature "xcmsRaw"

Thanks in advance.

Cheers
plasma33
3
XCMS / xcmsSet Feature Detection Details
Hi guys,

I need complete details of xcmsSet Feature Detection. I need information like what different sorts of methods are used and what all other features do the xcmsSet have etc.

Feature detection More Details plz->

    method : centWave
    ppm 30
    snthr 6
    peakwidth 10 60
    mzdiff 0.01
    prefilter peaks 3
    prefilter intensity 100

Is there any manual that provides some info.

Thanks in advance.

Cheers
plasma33
4
XCMS / Calculate Intensity/Abundance
Hi Guys,

How am I suppose to calculate intensity/abundance? Is it calculated from m/z and retention time? Can someone please help me.

Cheers
plasma33
5
metaXCMS / Raw Data Alignment Error
Hi Ralf,

I am getting error while performing "Raw Data Alignment". I am providing a screenshot of the error I am getting. Please suggest as in what should I do?


Cheers
Plasma33
6
Other metabolomics resources / LC-MS Raw Data
Hi Guys,

I am actually looking to download raw data from the Internet. I am actually looking for LC-MS data for E. Coli. It would be preferred if I we get raw data for metabolites i.e. for small molecules. I am not looking for raw data of any peptide or protein. Also is there any repository for LC-MS data based on metabolites? Thanks guys in advance.

Cheers
Plasma33