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Messages - yguitton

1
Courses and training / [Course] Workflow4Experimenters 2023
Processing, statistical analysis, and annotation of metabolomics data is a complex task for experimenters since it involves many steps and requires a good knowledge of both the methodology and software tools. The Workflow4metabolomics.org (W4M) online tool suit provides a user-friendly environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, FIA and NMR analysis. Such features are of major values for teaching computational metabolomics to experimenters, and previous courses using W4M since 2014 have been very successful.

For this new session, the proposed format evolves:
- From 06 to 10/03: theoretical sessions in videoconference from 10AM to 12PM each day
- From 20 to 24/03: practical sessions and tutoring, with the 1st hour of each day dedicated to short reminders and participant questions (following the theoretical session).

Info: https://workflow4metabolomics.org/w4e2023

Pre-Registration: https://sondages.inrae.fr/index.php/114793?lang=en (deadline 31/12/2022)

Goals: During this course, participants will learn how to use the W4M infrastructure to analyze their own dataset. Online sessions will be dedicated to methodology and tools. Face-to-face sessions will be devoted to tutoring. For these practical sessions, the participants will work on their own data (prerequisite for the training is to have a data set).

Date:
from March, Monday 6 to Friday 10 2023: 10-12 am (Paris hour): theoretical sessions
from March, Monday 20 (lunch time) to Friday 24 (lunch time) 2023: practical sessions
2
XCMS / Re: Getting UV data into XCMS+ findPeaks
Hi Steffen,

thanks for your answer, my xcmsRawUV function takes every time points as scan and every wavelength as m/z

my input matrix is
RT wavelength i ........ wavelength n
0.01 intensity i ...........intensity n
.
16.1 intensity ............intensity

scantime<- column RT values * 60
mz<- wavelength
tic<- sum of intensity for each RT

I have solved one of my problems (in fact there was an error in raw@tic allocation in my xcmsRawUV function)
so now,
I can draw good chromatogram with the code >plotChrom(object, mzrange=254), here the chromatogram is the one corresponding to 254 nm wavelength  and is exactly as expected. [attachment=1:2awapdi0]plotchrom_mzrange254.jpg[/attachment:2awapdi0]

and i can launch a
findPeaks.matchedFilter(raw..)
 but my function is still wrong somewhere (in the profile matrix?)
I think that part of my problem is  my profile matrix,
raw@env$profile<- transposition of my input matrix (without RT column)
 because findpeaks look at the column of the raw@env$profile matrix, right?

[attachment=0:2awapdi0]findpeaks_254.jpg[/attachment:2awapdi0]

I have some more work to do on my function if i want it to be able to find/align/compare peaks in my UV data as xcms does for mass data
 
May be someone have tried to do similar functions in R and can give me some clues?

thanks

Yann

[attachment deleted by admin]
3
XCMS / Getting UV data into XCMS+ findPeaks
Hi everyone,

I would like to know if someone tried to import UV data in XCMS and then used the findPeaks function?
I have seen on the forum that some xcms users are familiar with import of UV data in xcms but i didn't see any clue on the cookbook or on the internet.

I have managed to fill an xcmsRaw object with my UV data and i can create chromatograms with plotChrom() but i didn't managed to use the findPeaks.matchedFilter(raw, ...) function
error messages
seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *  :
  invalid (to - from)/by in seq(.)
1: In min(x, na.rm = na.rm) :  no argument find for min ; Inf
2: In max(x, na.rm = na.rm) :  no argument find for max; Inf

any idea?

to fill my xcmsRaw object i have tried to fill as many slots as possible but some are still empty.
#empty slots
raw@profparam
raw@polarity
raw@gradient
raw@msnAcquisitionNum
raw@msnCollisionEnergy
raw@msnPrecursorCharge
raw@msnPrecursorIntensity
raw@msnPrecursorMz
raw@msnPrecursorScan
raw@msnRt
raw@msnScanindex
raw@profmethod