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Messages - meow

17
XCMS / Re: xcms & mzR installation problem
I just tried setting up my typical R environment on a new computer, i.e. R 2.15 and the current bioconductor-devel versions of XCMS and mzR. I installed with

Code: [Select]
source("http://bioconductor.org/biocLite.R")
biocLite("mzR")
useDevel()
biocLite("xcms")

The versions look right in the library; however, there seems to be a problem with mzR. When I attempt to load mzR, the first attempt fails with an error message. Note: this is true for both the 64- and 32-bit versions of R.
Code: [Select]
> library(mzR)
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: value[[3L]](cond)
  error: failed to load module Ramp from package mzR
could not find function "errorOccured"
Error: package/namespace load failed for ‘mzR’

Interestingly, when I try the exact same thing again in the same session, R crashes:
Code: [Select]
> library(mzR)
Problemsignatur:
  Problemereignisname: APPCRASH
  Anwendungsname: Rgui.exe
  Anwendungsversion: 2.151.59607.0
  Anwendungszeitstempel: 4fe47a63
  Fehlermodulname: mzR.dll
[...]

Now I tried to download it by hand and reinstall, but I get the same problem:
Code: [Select]
> install.packages("D:/mzR_1.3.7.zip")
Installiere Paket(e) nach ‘D:/R/win-library/2.15’
(da ‘lib’ nicht spezifiziert)
leite 'repos = NULL' aus dem Dateinamen ab
Paket ‘mzR’ erfolgreich ausgepackt und MD5 Summen abgeglichen
> library(mzR)
Lade nötiges Paket: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: value[[3L]](cond)
  error: failed to load module Ramp from package mzR
konnte Funktion "errorOccured" nicht finden
Fehler: Laden von Paket/Namensraum für ‘mzR’ fehlgeschlagen
>

Right now I'm trying to build from source.
18
XCMS / Feed raw input data to XCMS? is now: deprofile.R
Hi,

a question: Say I have raw high-resolution .mzML files in profile mode. I don't want to convert them to centroid mode because I want to retain the additional profile information present (e.g. for fine isotope analysis later on). Now I can open this file in R using mzR, and I have written a function which computes a centroid-mode spectrum for every scan.

How can I provide the centroided data (generated directly in R) to XCMS in an xcmsRaw-like object, so I can run centWave on it?

(One reason why I want to do this is that the error obtained by taking the local intensity maxima for the "centroid" m/z value can become quite large. The obtained m/z is much more accurate if I use e.g. an algorithm like the "Exact Mass" algorithm from MZmine, which takes the FWHM m/z value.)
20
XCMS / massifquant not working
Hi,

We wanted to try the massifquant peak detection on some of our samples; apparently the findPeaks.massifquant function is not found in the DLL (the R part of the function seems to exist, it seems to fail when calling the DLL...)

Code: [Select]
fn <- "my_long_filename"
# just to try:
xs <- xcmsSet(fn, method="centWave")
# works great. However:
xs <- xcmsSet(fn, method="massifquant", ppm=5)
100309_pos_micropoll_19:
Fehler in .Call("massifquant", object@env$mz, object@env$intensity, object@scanindex,  :
  C Symbolname "massifquant" nicht in der DLL für Paket "xcms"

Code: [Select]
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)

(tl;dr)

mzR_1.0.0
xcms_1.30.0

The same was true for R 2.14.1 and XCMS 1.30.3.

Is the function not yet active, or is something wrong with our R?
(R for Windows, btw.)
21
XCMS / Re: TIC of MS/MS spectra?
Hi Steffen,

I looked into the source code to understand the issue.

Actually, my actual "problem" is caused by msn2ms (xcmsRaw.R, line 1873):

Code: [Select]
    object@tic <- rep(0, length(object@msnAcquisitionNum)) ## 

msn2ms just fills my TIC data with zeroes... apparently this is because the data is never read into xcmsRaw in the first place. Is there a special reason for this? The mzXML files themselves do contain the information.

---------------------------------------------
Concerning split.xcmsRaw: I now see why the function gives this warning in general. However, I did not call the split function myself; it is called by xcmsRaw(..., mslevel=2), xcmsRaw.R, line 85, where the xcmsRaw object is split into the TRUE and FALSE datasets (TRUE being all entries which have the correct @msnLevel).

The warning additionally confused me because MSn data is actually never dropped; it is just copied over verbatim without being split. (xcmsRaw.R, line 1809). Is this intended?

From an user perspective, it is not obvious why calling a method which is meant to transfer MSn data to MS1 slots (i.e. xcmsRaw(..., msLevel = n) results in a warning about MSn data being dropped (irrespective of whether or not the data is actually dropped)...  Would it maybe make sense to suppress the warning in this case?

Best,
-Michael
22
XCMS / TIC of MS/MS spectra?
Hi,

I'm basically trying to extract the TIC for each single MS/MS scan from my data file.

I tried using the xcmsRaw class, loading the MSMS data to the "main level" and looking at the TIC slot, but it appears to be empty (see code below; all other information seems to be correct.) Also, I don't understand what the warning message is telling me - is the function supposed to be used differently? Using mslevel=2 without includeMSn=TRUE returns NULL.

Code: [Select]
> xrmsms <- xcmsRaw(fileName, includeMSn=TRUE,mslevel=2)
Warnmeldung: In split.xcmsRaw(object, f = object@msnLevel == mslevel) :  MSn information will be dropped
> length(xrmsms@tic)
[1] 2562
> which(xrmsms@tic != 0)
integer(0)
> which(xrmsms@scantime != 0)
  [1]    1    2    3    4    5    6 etc etc until 2562

I would need this data to merge it with a dataframe generated from @msnScanindex and @msnPrecursorMz so that I could then filter out the intensity of the tandem spectra for one selected mass.

Any suggestions?