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Messages - hsiang

1
XCMS / What's definition of density in the process of group?
Deal all,

As mentioned of XCMS preprocessing document, the argument of group(), sleep, is enabled to plot the corresponding peaks. My questions are:

    1. Is the method "density" the default grouping ?
    2. What's the definition of density (Y-axis)? Is it normalized? If YES, what is the value normalized? Why the corresponding value is usually small?
    3. What's the definition of the solid line in this figure? Peaks are plotted as points showing it relative intensity. And what's meaning of the solid line?

Thank you for your reply. :)

Best regards,
Hsiang
2
XCMS / Re: How to repeat the workflow of XCMS Online by XCMS manual
Here I will report some of my examination.

The following R code is now successfully running.
Code: [Select]
files <- list.files(FILEPATH, full.names=TRUE, recursive=TRUE)
xset <- xcmsSet(files, method="centWave", prefilter=c(3,100), ppm=30, peakwidth=c(10,60), snthresh=6)

Comparing with Ricca's code, some parameters was modified in my solution.
    1. Attribute of polarity should be removed.
    2. "snthr=10" should be modified as "snthresh=6"

Now, the step of xcmsSet had been worked.  :)

However, I found that the detected number of features (peaks) for each sample is inconsistent with, i.e. a little more than, that produced by XCMS Online. I guess that the number of detected features in the log file provided by XCMS Online had been trimmed due to the retention time correction and peak alignment. But I am not sure.

Besides, while adding attribute of polarity to xcmsSet, the error message I mentioned before - error function (classes, fdef, mtable): unable to find an inherited method for function "findPeaks", for signature "NULL", will be shown. Actually, the polarity is an argument of xcmsSet, not of findPeaks.centWave. Therefore, I reasonably guess that was caused by  inheritance problem of R package.

    xcmsSet(files = NULL, snames = NULL, sclass = NULL, phenoData = NULL,
            profmethod = "bin", profparam = list(),
            polarity = NULL, lockMassFreq=FALSE, start=0,
          mslevel=NULL, nSlaves=0, progressCallback=NULL,...)


As previous guess, I still can not confirm my thoughts, because I am not really familiar with R language. If someone could solve my questions, I really appreciate your response.

Best regards,
Hsiang
3
XCMS / Re: How to repeat the workflow of XCMS Online by XCMS manual
Quote from: "Ricca"
Hope this help:

Code: [Select]
files <- list.files(path=myPath, pattern="xml", full.names = TRUE, recursive = TRUE)
xset <- xcmsSet(files, method="centWave", polarity="positive", prefilter=c(3,100), ppm=30, peakwidth=c(10,60), snthr=10)
xsetR <- retcor(xset, method="obiwarp", profStep=0.1, plottype="deviation")
xsetR <- group(xsetR, bw=5, mzwid=0.025, minfrac=0.5, minsamp=1)
xset.finale <- fillPeaks(xsetR)

I aloso suggest to read THIS
Best

Dear Recca,
Thanks for your suggestion. I had tried above codes line by line. However, while running the second instruction, there was an error message.
Quote
ko15: error function (classes, fdef, mtable) :
unable to find an inherited method for function "findPeaks", for signature "NULL"
Is there any configuration modified? Or I neglect something else?
The version and platform of my R:
    R version 2.13.1 (2011-07-08)
    Platform: i386-pc-mingw32/i386 (32-bit)
    OS: Windows 7

Best regards,
Hsiang
4
XCMS / How to repeat the workflow of XCMS Online by XCMS manually??
I am beginner of studying how to manipulate and process the LC-MS data.
I am curious how can I manually apply XCMS to access LC-MS data in processing of feature detection, retention time correction, peak alignment (grouping), peak filling just like workflow as XCMS Online. To learn the manipulation and processing of the LC-MS data, I apply the data from Saghatelian et al. which consists of 6 knock-out and 6 wild-type samples. I upload and process these data through XCMS Online. The corresponding log shows as below:
    General parameters
      polarity     positive
          retention time format     minutes
    2. Feature detection
      method : centWave
          ppm     30
          snthr     6
          peakwidth     10 60
          mzdiff     0.01
          prefilter peaks     3
          prefilter intensity     100
          Feature detection results :
        wt15.CDF    [1_WT]     -->  3515  Features.
           wt16.CDF    [1_WT]     -->  3499  Features.
           wt18.CDF    [1_WT]     -->  3033  Features.
           wt19.CDF    [1_WT]     -->  3047  Features.
           wt21.CDF    [1_WT]     -->  2850  Features.
           wt22.CDF    [1_WT]     -->  3235  Features.
           ko15.CDF    [2_KO]     -->  3516  Features.
           ko16.CDF    [2_KO]     -->  3553  Features.
           ko18.CDF    [2_KO]     -->  3097  Features.
           ko19.CDF    [2_KO]     -->  3087  Features.
           ko21.CDF    [2_KO]     -->  3109  Features.
           ko22.CDF    [2_KO]     -->  3201  Features.
    3. Retention time correction
      method : obiwarp
          profStep     0.1
    4. Alignment
      method : peakgroups
          bw     5
          mzwid     0.025
          minfrac     0.5
          minsamp     1
    5. FillPeaks
    6. Diffreport
      class1     1_WT
          class2     2_KO
          statistics.threshold.pvalue     0.01
          statistics.diffReport.value     into
    7. Additional Plots & Statistics
I try to use XCMS instruction xcmsSet to prepare analyte data from these LC-MS data jsut like as following.
Code: [Select]
library(xcms)
PATH <- "ms_netcdf/"
files <- list.files(PATH, pattern="*.CDF", recursive=TRUE, full.names=TRUE)
xset <- xcmsSet(files)
The problem is
    According to previous code, total number of peaks is 4721 generated by
xcmsSet constructor which is not consist with the result shown in previous log file. I guess that XCMS automatically construct the xcmsSet object. The procedure maybe contain several individual steps such as xcmsRaw, retcor, group. How can I reproduce the same results provided by XCMS Online?[/list]
I had also tried to detect feature by using the following instructions
Code: [Select]
wt15 <- xcmsRaw("ms_netcdf/WT/wt15.CDF");
wt15.cw.peakList <- wt15.wt.peakList <- findPeaks.centWave(wt15, ppm=30, snthresh=6, peakwidth=c(10, 60), mzdiff=0.01, prefilter=c(3, 100))
The number of peaks detected is also 3515 which is consist with XCMS Online log file. So I repeat the previous code for data loading and peak detecting of each sample. The following problem is how to do retention time correction? According to help of XCMS document, I found instruction of retcor.obiwarp. However, this instruction belongs to xcmsSet-class method. How can I perform the following retention time correction? This really confused me. Please give me your advising.
Thanks for all.

Best regards,
Hsiang