User: bhgyu

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bhgyu20
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Posts by bhgyu

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Comment: C: ReadMSData problem with xcms
... Worked perfectly! Thanks so much Johannes! ...
written 7 days ago by bhgyu20
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ReadMSData problem with xcms
... Hello,  I cannot work out how to make the readMSData function work? I get an error message. Anyone had this before and know how to solve it? Cheers! temp = list.files(pattern="*.CDF") readMSData(temp, pdata = pheno) Polarity can not be extracted from netCDF files, please set manually the polari ...
xcms readmsdata written 7 days ago by bhgyu20 • updated 7 days ago by Johannes Rainer1.1k
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Package won't recognise raw data files
... Hi guys,  I'm running the CAMERA package from bioconductor.  I've created an xcmsSet by c-binding multiple single xcmsSets, which all works fine. However, when I then later come back to the saved session to do annotation, Camera throws in the following error: xsaC <- groupCorr(xsaF) Start gr ...
metabolomics camera R written 8 days ago by bhgyu20
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Comment: C: 'names' attribute [12] must be the same length as the vector [6]
... Hi yes correct - 12 data files and 12 distinct names ...
written 28 days ago by bhgyu20
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Comment: C: 'names' attribute [12] must be the same length as the vector [6]
... It's this. It's an odd error especially cause I've run this with a similar dataset without these issues before... class(raw) [1] "OnDiskMSnExp" attr(,"package") [1] "MSnbase"     ...
written 28 days ago by bhgyu20
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'names' attribute [12] must be the same length as the vector [6]
... x <- findChromPeaks(raw, param = cwp) Error in names(res) <- nms : 'names' attribute [12] must be the same length as the vector [6] I don't understand the error above. I can't seem to figure out what this refers to or how to fix it? Happens on xcms. Strange though, this same code worked f ...
xcms R vector written 28 days ago by bhgyu20
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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 29 days ago by bhgyu20
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Comment: C: XCMS obiwarp adjustRtime issue
... Ooo lala it worked :-)   ...
written 4 weeks ago by bhgyu20
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Comment: C: XCMS obiwarp adjustRtime issue
... Thank you! Will give this a shot and report back. ...
written 4 weeks ago by bhgyu20
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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 4 weeks ago by bhgyu20

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