Sorry, I didn't see your message earlier. The LBM file is just a text file and you can read that into R. If you're interested in the code I used, just let me know.
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.
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.
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
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