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Messages - Jan Stanstrup

1
XCMS / Re: Howto re-integrate with new rtborders?
I haven't tried to manipulate it like that so I don't know.

But your peakwidth is too narrow I think if you want all in one. You have a max of 10 sec. If you want to merge all you need several minutes I assume. At least I'd try that.
2
XCMS / Re: Howto re-integrate with new rtborders?
One way to achieve this, I think, is to set mzdiff to something positive. That should make everything connected integrate as one. Of course this might have unwanted effects in other places.
3
XCMS / Re: Optimize peak-picking
I think this is gonna be very difficult to achieve with so much overlap. What I would try is lowering the minimum peakwidth. If that doesn't work last resort is trying matchedfilter instead of centwave.
6
http://www.moviss.eu/

When: Sept 25-27 2017
Where: Vorau, Austria
To register and for more information, go to www.MOVISS.eu, and follow us on Twitter @MOVISSmeet

More information:
We would like to invite you to Bio&Data, the first workshop of the newly established MOVISS - "Mountain Village Science Series" taking place in Vorau, Austria (Sep 20-23, 2017). MOVISS Bio&Data is different to the usual conferences. It is rather constructed as a small, problem-driven meeting, full of discussions and questions about how to deal with metabolomics data reasonably. In this way, we hope to constructively engage some of the greatest minds collaboratively in solving some of the challenges of the metabolomics and bioinformatics community.

Four sessions are planned, each devoted to a separate step of the metabolomics process; Design of Experiments, Analytical Analysis, Data Processing and Statistical Analysis in the biosciences will all be discussed including your data if you bring them for discussions.

We plan a summary of this discussion will be produced as a paper for publication to share within the wider metabolomics community. Finally, you can continue with the R Summer School from September 25 - 27, 2017 in Vorau!
7
Conferences and seminars / Metabomeeting 2017
The 10th Metabomeeting will be held at the University of Birmingham in the UK on the 11-13th December 2017.

The deadline for oral presentation abstracts is 15th July 2017
The deadline for poster abstracts is 1st October 2017.


The meeting agenda will be available on the conference web-site and will include sessions on some or all of the following:
  • Applied Metabolomics 
  • Drug Discovery and Development
  • Human Disease and Nutrition 
  • Microbial, Invertebrate and Environmental applications 
  • Plants 
  • Data Analysis and Integration with Systems Biology 
  • Metabolite Identification 
  • Data Modelling and Data Interpretation 
  • Workflows and Computational Metabolomics 
  • Analytical Approaches and Developments 
  • Lipidomics
  • Stable Isotope Metabolomics and imaging
  • Lipidomics
  • Method standardisation 
  • Early career scientists

Link: http://metabomeeting2017.thempf.org/
8
Announcements / Metabolomics Society conference 2017

Join your Metabolomics peers in 2017!

We are delighted to announce that Early bird registration is open for Metabolomics 2017 - the 13th Annual Conference of the Metabolomics Society. We look forward to seeing you in Brisbane! Please visit the new website for more information and take advantage of the early-bird pricing.

Website:
Metabolomics 2017

Hosted by: The Metabolomics Society
Where: Brisbane, Queensland, Australia
When: June 26-29, 2017

Abstract submission information will be published within the next month. We look forward to seeing your latest findings!

The Society has obtained a group block of hotel rooms, visit the Hotel page of the website to view several different options. You are encouraged to book your hotel accommodation as soon as possible, since June is a very busy time inBrisbane.

Happy New Year!
The Metabolomics 2017 Planning Team
9
XCMS / Re: How to export Xset object intensity data?
I have not been aware of intf since I am normally using centwave that doesn't have this concept. I am using into because when I compared to intb the CAMERA grouping was better with into suggesting that was a more stable measure.

As for intf vs into I cannot answer but I guess it depends how good the fitted model is.
10
pic3 looks like shoulder peaks. But difficult to see when I only have that zoom level.
What you need to do is take one of the largest peaks, look at the spectra, zoom in around the mass peak at low intensity. If you see a lot of small peaks (1-5%) around the real peak --> that is shoulder peaks and you need to filter them before an analysis.

0.0005 sounds too narrow to be to compare peak tables. 0.0025 seems more reasonable. The tools might choose the mass differently (at apex, mean/median across the peak, mean/median across samples).

16238 seems like a lot of features. Suggests to me something is up. Could be if there are many shoulder peaks, if you detect a lot of noise, or chop up peaks like mzmine did.

I am not familiar enough mzmine to tell you what to tweak but it makes sense if the other tools give you 1 or 2 peaks for that noisy peak.
11
XCMS / Re: How to export Xset object intensity data?
Are you looking for the peakTable function or am I misunderstanding what you are trying to do?
If you use CAMERA the equivalent function is getPeaklist.

fillpeaks peaks are in @peaks yes.

I would think into is the most common.

I don't think there is a real benchmark available anywhere. Difficult to establish a ground truth. It is always a compromise.
12
XCMS Online / Re: CAMERA annotation
I think the XCMS online people rarely come by here so you might consider contacting them directly: https://xcmsonline.scripps.edu/landing_page.php?pgcontent=contact

As for the annotations the isotope annotation and adducts/fragments are two different steps and the adducts/fragments is the computationally intensive one they seem to have limited.

Of course another option would be using XCMS through R so you have control...
13
I assume these examples are not from the same file?

Also how did you compare the masses? Which tolerance? Surely there must be some overlap.

The warning about profile mode might be due to too low ppm setting or orbitrap shoulder peaks: http://www.metabolomics-forum.com/index.php?topic=1044.msg3019#msg3019
You are getting the inserting error thing? If just few you can ignore.
14
XCMS / Re: Inconsistent integration borders in EICs
If you don't wanna try to install the package you could do:
Code: [Select]
source("https://raw.githubusercontent.com/stanstrup/chemhelper/master/R/xcms_helpers.R")


In that case you'd have to decipher the help page from here: https://github.com/stanstrup/chemhelper/blob/master/man/analyze.xcms.group.Rd
15
XCMS / Re: Inconsistent integration borders in EICs
I think there is a number of newer functions for useful visuals but I have not used them yet.

For the grouping step I have written a function I find useful: http://www.metabolomics-forum.com/index.php?topic=577.msg1789#msg1789

You can also see where peaks where found with that.

I am having some dependency problems with my package so it might be easier to get the function (analyze.xcms.group) directly from: https://github.com/stanstrup/chemhelper/blob/master/R/xcms_helpers.R