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Messages - cbroeckl

1
R / Re: DOUBT ABOUT MS^E
Jan,

I can't say that I remember how this worked, though I think I did try it.  If I recall, the problem is that you have to know which scan events (by integer number) are MS and which are MSE and which are LockMass.  I think that if you have that data, or can extract it in an efficient manner, it would work, but I never figured out an efficient way.  Not to say it can't be done, I just haven't done it.

Corey
2
Other / Re: Access NIST library from R or similar
Hello Jan,
There is a way to get data out, but it isn't trivial.  NIST provides .dll packages which can be used for third party software integration.  They are available by request from NIST, and are the tools that companies like Waters and Agilent and Thermo incorporate spectral searching of the NIST library into their software.  We used it when we build RAMSearch.  Unfortunately, I did not write that code and I do not know the details of how difficult it is to incorporate.  I do know that the people that did write the code complained about it...  Big caveat - NIST DOES NOT SUPPORT THIS CODE!  They know it works, but they are not going to provide much in the way of advice as to how to use them.  I think that they are also not freely distributable, but I cannot be certain that is the case. 

Corey
3
R / Re: DOUBT ABOUT MS^E
Francisco,

The problem with using proteowizard is that I am pretty sure waters tags their MSe data as 'MS1' - the logic being their is no precursor selection.  Since the data are not tagged as MS2, the proteowizard filters do not work.  I use proteowizard whenever i have either MS1 data only, or MS1 data with dedicate MS/MS data.  For MSe I still use databridge run from the acquisition sequence table.  If you have found a solution within proteowizard for MSe with the goal of bringing it to XCMS, do let me know, as I would be very interested in trying it out as well.  

Corey
4
XCMS / Re: sequential addition of files to an xcms object
Thanks edmandsw,

I currently am using a custom script for feature grouping which simply assumes that if retention times overlap and mass windows (plus a given ppm error) overlap, the represent the same compound.  After each iteration, I apply a retention time adjustment  as well.  The tried-and-true XCMS functions are just much more well used and validated than my internal tools, so I was hoping there would be a way to utilize them that I had missed.   I will look at the package you are developing - it does look interesting! Are you aware of the skyline/panorama tool sets?  I know they are also working on vendor neutral QC monitoring.  Interested to see how yours compares.  

Corey
5
XCMS / Re: peak shape/symmetry?
I have done filtering for peak width: 

    orig<-xset@peaks
    good<-which((orig[,"rtmax"]-orig[,"rtmin"])<(3*maxpw))
    filt<-orig[good,]
    xset@peaks<-filt

No reason it could not be adapted for shape descriptors.  It has to be done before grouping.
Corey

6
XCMS / sequential addition of files to an xcms object
I am interested to know whether there is a way to sequentially add files to an xcms object.  for example, I am running XCMS, I have completed feature finding on 10 files, and have the features grouped with retention time correction.  I now want to add file 11 to this xcms object.  From what I can tell, adding file 11 basically means that all the grouping and retention time correction are wiped from the xcms object to enable addition of an 11th file.  Is this accurate, or is there a way to do this that I am not thinking of?  Thanks,Corey
7
XCMS / Re: Problems with the fillpeak step
Just tested new R (3.3.1) and older XCMS (1.46.0) and the error is gone.  I will be using this version until a newer is released. 
Corey
8
XCMS / Re: Problems with the fillpeak step
Also having this problem in the density step:  'error in density.default(speakmat[,"rt"], bw, from='retrange[1]-3*: 
non-finite 'from'

I reverted to an xcms installation from a previous R version and the problem went away on the same dataset, so I think it has to do with a new XCMS version.  I can't say for certain it isn't also dependent on a new R version at this point.  

Functional:
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xcms_1.40.0         Biobase_2.24.0      BiocGenerics_0.10.0 mzR_1.10.7          Rcpp_0.12.1        

loaded via a namespace (and not attached):
[1] codetools_0.2-8 tools_3.1.1 


NONFUNCTIONAL: 
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xcms_1.48.0         Biobase_2.32.0      ProtGenerics_1.4.0  BiocGenerics_0.18.0 mzR_2.6.2           Rcpp_0.12.5        

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 codetools_0.2-14   grid_3.3.1         lattice_0.20-33  
9
XCMS / Re: MRM data?
Hello XCMSers -
Just wanted to see whether there is anyone out there who has thus far figured out XCMS for MRM data.  Thanks,
Corey
11
XCMS / Re: memory error during fillpeak step
Steffen et all,

I just started testing the fillPeaks step using R v 2.15.2, xcms v1.34.0.  I haven't completed the process yet, but I am 99.9% certain that this version will complete the fillPeaks step on the dataset I began earlier.  I am ~10% through the data files and the memory usage by R has hardly changed over that time.
I will update this when I know for certain whether it succussfully finished.
Corey
12
XCMS / Re: memory error during fillpeak step
nSlaves=1 still fails.  I don't know how far it gets, but the memory climbs pretty quickly until I receive the same error message as before.
13
XCMS / Re: memory error during fillpeak step
I just wanted to refresh this thread with my own memory problems:
Windows 7 machine, 64 GB RAM
R 3.0.2
xcms 1.38.0

> xset
An "xcmsSet" object with 1610 samples

Time range: 1.7-1205.4 seconds (0-20.1 minutes)
Mass range: 55.0152-1199.8425 m/z
Peaks: 7274098 (about 4518 per sample)
Peak Groups: 6469

Memory usage: 1360 MB


xset <- fillPeaks.chrom(xset, nSlaves=2)
Error: cannot allocate vector of size 39.7 Mb

Windows task manager has the memory full upon failure, which gc() cleans up.
14
XCMS / sigma fitgauss question
I am using the centwave algorithm for peak detection, selecting the 'fitgauss=TRUE' option.  I am curious to know how best to interpret the values output by fitgauss - in particular sigma.  In the centwave algorithm, there is an parameter specifying the min and max peak width, in seconds - I usually use something like c(2:20) for UPLC.  When I look at the gaussian sigma values returned, it has raised two questions for me:

1. why are there peaks in the resultant xcms dataset for which the sigma values is larger - sometimes by an order of magnitude - than the max peakwidth setting?
2. how do I interpret sigma values of 'NA'. 

I am guessing that the answer to the latter question is that the gaussian fit is bad, and no mu/sigma/h can be returned. Any insight is appreciated.

Corey
15
XCMS / Re: retrieve an averaged spectrum
steffen,

THanks for the tips.  I used the links you provided, and in the mzClust.R file under R, there is code:

Code: [Select]
mzClustGeneric <- function(p,sampclass=NULL,
                          mzppm = 20,
                          mzabs = 0,
                          minsamp = 1,
                          minfrac=0.5)

I did find the code snippet you quoted in the xcmsSet.R file. 

Is it safe to assume that everything necessary to run xcmsSet() from the R console is located in the xcmsSet.R file?  If not, how do I recognize calls to other files?  Thanks again,  being able to see all the details should allow me to understand everything (including how to properly write R code) better.
Corey