User: bhgyu

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bhgyu30
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Posts by bhgyu

<prev • 34 results • page 2 of 4 • next >
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Comment: C: XCMS obiwarp adjustRtime issue
... Thanks for your help! Oh and if you have any recommendations for settings adjusted for Q-TOF for these new functions, let me know. I'm using as much as I can from my settings for the older xcmsSets, but the new workflow is quite a bit different and there's not much info out there as to adjustments. ...
written 12 weeks ago by bhgyu30
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Comment: C: XCMS obiwarp adjustRtime issue
... Ooo lala it worked :-)   ...
written 12 weeks ago by bhgyu30
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Comment: C: XCMS obiwarp adjustRtime issue
... Thank you! Will give this a shot and report back. ...
written 12 weeks ago by bhgyu30
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Comment: C: XCMS obiwarp adjustRtime issue
... Hi Johannes, Thanks for the reply. Here's the full sessionInfo. Sadly I won't be able to share the data - not my data and 12GB. I did try various binSizes, but that didn't work :-( Could it be somewhere in the initial upload steps? Maybe it has to be binned before being RT corrected?   R vers ...
written 12 weeks ago by bhgyu30
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XCMS obiwarp adjustRtime issue
... Hi guys, I can't seem to find an answer to this issue. It has been flagged before but without a successful solution. cwp <- CentWaveParam(peakwidth=c(5,20), ppm=15, snthresh=5, prefilter = c(0,0)) xod <- findChromPeaks(raw, param = cwp)​ xod <- adjustRtime(xod, param = ObiwarpParam()) ...
metabolomics xcms obiwarp adjustrtime written 12 weeks ago by bhgyu30 • updated 12 weeks ago by Johannes Rainer1.1k
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MAIT or Specmine
... Hi there,  Has anyone gotten either MAIT or Specmine to work?  I can't seem to able to load the data into the suggested formats. Neither will recognise CDF files in a specified data directory. There's sadly not much info on these out there... ...
metabolomics mait mass spectrometry specmine written 3 months ago by bhgyu30
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Jackknifing/bootstrapping input and output question
... I'm trying to perform jackknifing or bootstrapping on the P-values from 6 data sets (which have previously been combined in a meta analysis). However, I'm not quite clear on the input and what the results are actually telling me.  My aim is to assess if my top genes will remain robust if I jackknif ...
microarray R bootstrap jackknifing written 6 months ago by bhgyu30
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Comment: C: RankProd crashing - stability issues?
... Sorry, Let's try this: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85426 The data set has to be large to test this so I cannot think of anything but an external one. Usually examples in R are rather small.  ...
written 7 months ago by bhgyu30
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Comment: C: RankProd crashing - stability issues?
... Hi Martin,  Thank you. I did the above yesterday. I updated R to 3.4 and RankProd to 3.2 Bear in mind though, this all does work with a data set that has only 20 samples. Add 180 and it keeps crashing.  I also should add that I did gave this a go on a more powerful computer with the same problem ...
written 7 months ago by bhgyu30
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Comment: A: RankProd crashing - stability issues?
... Ok thank you. ...
written 7 months ago by bhgyu30

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