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Messages - sneumann

61
XCMS / Re: xcmsRaw and obiwarp
Hi,

the quick answer is "no". What's wrong with an xcmsSet ?

Yours,
Steffen
62
XCMS / Re: Correction of retention times 'by hand'
Hi,

you could write a small script that loads the CDF or mzData,
and modify the xcmsRaw@scantime slot, and afterwards
write the data back with write.cdf() write.mzdata().

Alternatively, you could try the retcor(method="obiwarp")

Yours,
Steffen
63
XCMS / Re: XCMS has a limit of 9999 scans?
Hi,

if you want to limit an xcmsSet to a certain (RT) range you can specify the scanrange=c(min,max) parameter,
where min and max are scan numbers (and not RT in minutes or seconds), so that depends
on the scan frequency.

Yours,
Steffen
64
XCMS / Re: memory error during fillpeak step
Hi,

Quote from: "gunnar"
fillPeaks seems to loose all values except mz, mzmin, mzmax, rt, rtmin, rtmax, into, maxo and sample.
I think that problem was fixed with

CHANGES IN VERSION 1.37.1
--------------------------
BUG FIXES
    o fixed fillPeaks, which 1) dropped non-standard columns
    and 2) failed if nothing to do, based on patches by Tony Larson.

Or is it still present there ?

Yours,
Steffen
65
XCMS / Re: XCMS has a limit of 9999 scans?
Hi,

can you give a more specific example ? A code snippet ? Possibly example data ?
What is "identify" ? Do you mean clicking into a plotChrom(ident=TRUE) ?

Yours,
Steffen
68
XCMS / Re: R 2.15.2
Hi,

I guess there is a segmentation fault somewhere loading the
required packages behind XCMS, so we need to find the culprit.

In your R-2.15.2/3 installation that crashes, try
Code: [Select]
library(Rcpp)
library(mzR)
library(xcms)

and post the output of sessionInfo() after the last non-crashing library loading.
I expect the crash to come from non-matching Rcpp and mzR versions.

It might also help (I have little experience with windows) if you start the
Windows command line, run the R command line version (without GUI)
and do the crash without the GUI. There might be more informative information.

Yours,
Steffen
69
XCMS / Re: Diffreport EIC's and scanrange
Hi,

1) which version of xcms is that ?  2) Can you reproduce the problem
with the faahKO data files ? Then we'll be able to see where the problem
comes from.

Yours,
Steffen
70
XCMS / Re: retrieve an averaged spectrum
Hi,

Quote from: "cbroeckl"
Stupid questions
Corey
There are no stupid questions!

Quote from: "cbroeckl"
I have never really accessed the behind the scenes code, and for the life of me I cannot find the file you refer to.
Corey

For Windows (and Mac ?) the package downloads are "compiled", that's why you don't see them.
Linux will download the sources and compile on-the-fly during installation.

The source code is in the "package source" e.g. xcms_1.34.0.tar.gz at http://bioconductor.org/packages/releas ... /xcms.html
Alternatively, you cen check it out with SVN from https://hedgehog.fhcrc.org/bioconductor ... acks/xcms/
Check out http://bioconductor.org/developers/source-control/ for the password.

If you made any changes to the sources, you then will need to
R CMD INSTALL /path/to/xcmssources/
and re-load xcms into R.

Yours,
Steffen
71
XCMS / Re: retrieve an averaged spectrum
Hi,

Quote from: "cbroeckl"
how to apply mzClust to to spectra.

Check out the mzClustGeneric in xcms/R/mzClust.R,
this is the function doing the actual work.

This is called from group(method="mzClust") and takes a simple mz/sample matrix.

Code: [Select]

          groups <- mzClustGeneric(peaks[,c("mz","sample")],
                                   sampclass=classlabel,
                                   mzppm=mzppm,mzabs=mzabs,
                                   minsamp=minsamp,
                                   minfrac=minfrac)


Quote from: "cbroeckl"
So I think that I either need to
1. extract individal scans from a raw data file so that they are inserted into an xcmsSet object or

This would be a new method for findPeaks(), which would be quite welcome!

For direct infusion with several scans (as opposed to single scans, which MSW expects)
I could envision that it is not too unlike centWave,
but without the wavelets (because there are no gaussian peak shapes):

It'd take a (very narrow) scanrange, detect ROIs, but skip the wavelet analysis,
and then apply one of the mzCenterFun to get a more accurate m/z than
you can expect from a single scan. A question would be whether and how
to integrate the intensities (Max ? Avg ?). Does that make sense ?

Yours,
Steffen
74
CAMERA / Re: Rdisop filter
Hi,

the filter argument was a start to implement sth. along the lines of what you want,
but not finished. To be honest, Rdisop is basically in maintenance mode.

You can select "valid" formulas with normal R operations:

Code: [Select]
data <- decomposeMass(180.063, ppm=50)

dbeidx <- data$DBE >0
nitrogenidx <- data$valid == "Valid"

data$formula[dbeidx & nitrogenidx]

Yours,
Steffen