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1
XCMS / Re: Saving the intermediate xcmsSet objects
Last post by nhabibi -
Dear Johannes

I save and load the xcmsSet object:

save(xset, file = "xset.RData")
xset = load("xset.RData")

But I think it needs type conversion after being loaded. Would you please tell me how to convert it to an xcmsSet object?

I just found type.convert(), but it dose not work in this case.

Thanks in advance
Narges

2
METLIN / Re: METLIN license
Last post by Simon -
Hi everyone. This is Simon Aloo from Korea.
I would like to inquire about the accessibility of the Metlin database system. Previously, we could easily access the ion fragment details whenever we search for a particular compound. This process made it easier to accurately identify compounds. However, currently, whenever I click the button of MS graphs, I am not able to see the picks of the fragments of a given compound. The names of different compounds come, but to identify them by comparing their peaks with database information is not possible. Please, if anybody has any solution, may I kindly know. I'll appreciate it so much.
Thank you all
5
XCMS / Saving the intermediate xcmsSet objects
Last post by nhabibi -
Hi all,

I am working on a metabolic dataset using XCMS pipeline.

Is there a way to save the intermediate xcmsSet objects as a file which can be loaded and used later by the needed functions? e.g. loading the result of the xcmsSet() inside the group().

Thanks
6
MS-DIAL / MrmprobsConsoleApp parameters
Last post by Ondrej -
Hi Hiroshi,
would it be possible to add a command line option to export the raw matrix data file?
Thank you.
Ondrej

Code: [Select]
Mrmprobs Console App requires the following args:
                                                MrmprobsConsoleApp.exe <analysisType> -i <input folder> -o <output folder> -m <parameter file> -r <reference library file> -d <dia dictionary file (required in abfdia)>
                                                Where: <analysisType>   is one of abfmrm, mzmlmrm, mzmlscan, abfscan, abfdia    (required)
                                                           <input folder>       is the folder containing the files to be processed      (required)
                                                           <output folder>      is the folder to save results   (required)
                                                           <method file>        is a file holding processing properties (required)
                               <reference library file>           is a file containing rt/transition/ratio/range information at tab-delimited text.
                               <dia dictionary file>    is required in DIA-data process containing SCAN/DIA ScanID MzBegin MzEnd information as tab-delimited text
7
Mass spectrometers / Cloud Plot - XCMS
Last post by adanie36 -
Hey everyone- I'm a grad student working on a new project. I am new to the forum and new to studying metabolomics. I have done some LC-MS work, and used XC-MS to do some data processing. I am just very confused as to what the meaning of the cloud plot is. I can't seem to find anything online that puts it in terms that are easy to understand. Can someone explain this plot? What is fold change? What does negative vs. positive mean in the cloud plot? Thanks so much!
9
MS-DIAL / Re: Long processing time issue with Waters data
Last post by rsamples -
Hi,
First, MS-DIAL now supports direct processing of the .RAW files without the need of prior conversion to .abf. Besides, do you mean each file is ~5 GB big or the total size of all your files? In the former case, I would guess that you have profile files? then the solution could be that centroid the file first using for example Masslynx.

Best,
Qizhi Su


Thank you, I did see that .RAW is an option in the import dialog however when I attempted to import the .RAW files they opened as folders instead of being read as files. Is there some kind of setting that needs to be changed for these to be seen as data files? I am on Windows.

Yes, each file is 5 gb, ~500 GB between all files. I will attempt to centroid the files in Masslynx, I didn't know this was an option but found Waters' documentation on it.

Thank you for the assistance.
10
MS-DIAL / Re: Long processing time issue with Waters data
Last post by QizhiSu -
Hi,
First, MS-DIAL now supports direct processing of the .RAW files without the need of prior conversion to .abf. Besides, do you mean each file is ~5 GB big or the total size of all your files? In the former case, I would guess that you have profile files? then the solution could be that centroid the file first using for example Masslynx.

Best,
Qizhi Su