User: bhgyu

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bhgyu20
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Posts by bhgyu

<prev • 30 results • page 2 of 3 • next >
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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 26 days ago by bhgyu20 • updated 26 days ago by Johannes Rainer1.0k
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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 4 weeks ago by bhgyu20
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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 4 months ago by bhgyu20
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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 5 months ago by bhgyu20
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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 5 months ago by bhgyu20
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Comment: A: RankProd crashing - stability issues?
... Ok thank you. ...
written 5 months ago by bhgyu20
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RankProd crashing - stability issues?
... Hi guys, Anyone know why RankProd crashes R Studio when there are more than say 100 sample cases?  It consistently crashes R Studio for experiments with a larger number of subjects.  No error code or anything. R just encounters a fatal error.  Cheers > sessionInfo() R version 3.3.2 (2016- ...
rankprod crash written 5 months ago by bhgyu20
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GSEA threshold question
... Hi guys, Would someone have an explanation for the following?  I've run multiple meta analysis and successfully did ORA at p < 0.05 However, whenever I try doing GSEA (using ReactomePA or clusterProfiler) it fails at p < 0.05 and only works at p < 1 (I'm using the Fisher's p val ranked g ...
clusterprofiler R gsea reactomepa written 5 months ago by bhgyu20
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Comment: C: GeneList issue ClusterProfiler
... Yes, always, to test things first. I only specify ones I'm happy it all works.  But my problem isn't the minSize, it was the p.value cutoff. ...
written 5 months ago by bhgyu20
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Answer: A: GeneList issue ClusterProfiler
... Hi there, thanks for the quick reply!  I did manage to get it working, but just wondering what the best p.value cutoff for Fisher's p.values is since I'm running a meta analysis so I cannot use single data set p values or logFCs, but have to work with the p-values from the combined analysis? I hav ...
written 5 months ago by bhgyu20

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