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Topics - ricoderks

1
XCMS / Show only few chromatograms
Hi all,

I thought I did this before, but just can't figure it out anymore. I have a read about 300 data files into xcms, but I only want to show the base peak chromatogram of few of them.

Code: [Select]
bpis <- chromatogram(object = raw_data, aggregationFun = "max")

This will get all chromatograms and I thought I could plot only 3 of them like this:

Code: [Select]
plot(bpis[c(1, 25, 50, 100)])

But this didn't work. Is there way to only show a few chromatograms while raw_data contains the data of about 300 files.

Cheers, Rico
2
MS-DIAL / convert lbm to lbm2
Hi,

Is it possible for me to convert a lbm file to lbm2? I added some lipids manually and the performance is a bit better when using the lbm2 file.

Cheers, Rico
3
MS-DIAL / MSDIAL crashes during data curation
Hi Hiroshi,

I'am having some issues with MSDIAL v4.18. I added my own lipids to the lbm database which I downloaded from your site. If I'am in the alignment spot viewer and set a spot (this spot is not correct identified it has w/o some lipid) to a lipid I added to the database and tick ref. matched MSDIAL crashes. If I do the same with a spot (did this with another spot) and set it to a lipid which was already in the original database everything goes fine.
I don't see anything weird that I added to the database, but to be sure this is the lipid I added.

Code: [Select]
NAME: lysoTAP 18:1_0:0
PRECURSORMZ: 488.359276662
PRECURSORTYPE: [M+2HCOOH-2H]-
FORMULA: C24H48NO3
INCHIKEY:
SMILES:
RETENTIONTIME: 5
IONMODE: Negative
COMPOUNDCLASS: Others
Comment: NA
Num Peaks: 3
281.2486        900
442.3538        10
488.3593        10

Do you maybe know what's going on?

Cheers, Rico
4
XCMS / fillPeaks gives a warning
Hi all,

When I run fillPeaks after I grouped everything I get several warnings. I first read the mzXML files witch xcmsSet, method=centWave. Then I group them with density method, next I do the fillPeaks which gives me these warnings :
Warning messages:
1: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-119_Column1_BC1_01_2805_ALIGNED.mzXML
2: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-128_Column1_GE7_01_2650_ALIGNED.mzXML
3: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-129_Column1_BD5_01_3181_ALIGNED.mzXML
4: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-130_Column2_GD2_01_2874_ALIGNED.mzXML
5: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-131_Column2_GD8_01_2884_ALIGNED.mzXML
6: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-133_Column1_GA7_01_2847_ALIGNED.mzXML
7: In FUN(X[[7L]], ...) :
  (corrected) retention time vector length mismatch for sample_1-139_Column1_BD1_01_2456_ALIGNED.mzXML

Can anyone tell me what is going wrong here?

I'am running R3.0.1 on a 64bit system.

Cheers, RICO
5
XCMS / problems installing on 64bit linux
Dear all,

I'am trying to install XCMS on a 64 bit linux system, but failing to do so. Immediatly after using the biocLite function to download XCMS I get the following warning :
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  argument 'lib' is missing: using '/home/rico/R/x86_64-pc-linux-gnu-library/2.11'
Warning: dependency âsnowâ is not available
also installing the dependencies 'faahKO', 'ncdf', 'rgl'

After packages are downloaded I get the following error :
* installing *source* package âfaahKOâ ...
** R
** data
** inst
** preparing package for lazy loading
Error in loadNamespace(name) : there is no package called 'xcms'
ERROR: lazy loading failed for package 'faahKO'

All other packages with the following errors :
configure: error: netcdf header netcdf.h not found
ERROR: configuration failed for package âncdfâ
* removing '/home/rico/R/x86_64-pc-linux-gnu-library/2.11/ncdf'

Anyone any ideas? Thanks in advance.

Cheers, Rico

My system is :
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8      LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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