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Topics - CoreyG

2
Conferences and seminars / EMN Webinar 20th November 2019 (15:00 UTC)
Coming up 20th November 2019 at 15:00 UTC (7:00 PST, 10:00 EST, 16:00 CET)!

Metabolomics as a tool for elucidating plant growth regulation

Rising demand for food and fuels makes it crucial to develop breeding strategies for increasing crop yield/biomass. Plant biomass production is tightly associated with growth and relies on a tight regulation of a complex signaling network that integrates external and internal stimuli. The main goal of our group is to elucidate the processes underlying plant growth and production of biomass by combining physiology, metabolomics, and gene expression analyses. In my presentation, I will provide examples of i) how the evolutionary conserved Target of Rapamycin pathway fine-tunes metabolic homeostasis to promote biosynthetic growth in plants; ii) the potential of metabolite profiles to predict plant performance as biomarkers.

Click here to learn more about this latest webinar by Camila Caldana (PhD).

Please register for “Metabolomics as a tool for elucidating plant growth regulation," to be held on 20th November 2019 at 15:00 UTC (7:00 PST, 10:00 EST, 16:00 CET) at: https://register.gotowebinar.com/register/5446228940397431052

After registering, you will receive a confirmation email with information about joining the webinar.

Brought to you by the EMN of the Metabolomics Society.

3
XCMS Online / Problems with XCMS Online? Look here
Dear Forum members and visitors,

We have been very happy to see users supporting each other to solve each others issues with XCMS Online. However, the number of users with detailed knowledge of XCMS Online has dwindled. This has left many unanswered questions in the forum.

To help those going forward, we recommend you to direct specific questions to the XCMS Online Contact Form.
It might also help to look at the online documentation.

For questions related to the R version of XCMS, please ask them in this board.
4
XCMS / Implementing custom retention time alignment algorithms
Hi Everyone,

We've been working on some retention time alignment algorithms, recently. The major driver for this, is that we have noticed that compounds from different classes can exhibit unique retention time drift behavior. So even though they initially elute at very close retention times, one class of compounds will begin to elute later in the chromatogram while the other class elutes earlier.

The issue we are facing, is how can we best apply these adjusted retention times to an XCMSnExp objects and still maintain all the capabilities of XCMS?

Currently, we can force the adjusted retention times into an XCMSnExp object by manually calling adjustedRtime. I know this isn't recommended practice, but is there an alternative? We don't want to use applyAdjustedRtime as we want to go back and integrate missed peaks.

For the most part, this appears to work well, except when we run fillChromPeaks. We get the following error:
Code: [Select]
> xdata<-fillChromPeaks(xdata,BPPARAM=SerialParam())
Defining peak areas for filling-in ....Error in if (idx_rt_adj > idx_pk_det) { : argument is of length zero

This appears to be produced when dropChromPeaks is called (fillChromPeaks->filterFile->chromPeaks->dropChromPeaks). Essentially, dropChromPeaks looks in processHistory to determine whether peak detection occurred before or after retention time alignment. But the retention time alignment isn't in processHistory.

I couldn't quite see how we can add entries into the processHistory. Eventually I resorted to fudging an entry to circumvent the error.
Code: [Select]
processHolder<-processHistory(xdata)
processHolder[[1]]@type<-"Retention time correction"
xdata@.processHistory<-c(processHistory(xdata),processHolder)
Is there a simpler way to accomplish this?

Would anybody care to offer some advice/suggestions for any part of this? I'm happy to have anyone's input.
Thanks!