User: garfield320

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garfield32020
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Posts by garfield320

<prev • 6 results • page 1 of 1 • next >
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XCMS - cannot allocate vector of size **Gb when global environment is empty
... I'm using 64bit R in Windows 10, and my current `memory.limit()` is 16287. I'm working with mass spectra files (mzXML), I've been calling individual files one at a time using the line below, which increases my `memory.size()` to 7738.28. Then I filter out noise using basic R functions, and plot t ...
xcms R written 8 weeks ago by garfield32020
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Comment: C: MSnbase extracting individual spectrum based on precursor ion m/z
... Yes that was the problem, `which(round(precursorMz(rawdata),4)==808.5253)` gave me the index I wanted, thanks! ...
written 3 months ago by garfield32020
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Comment: C: MSnbase extracting individual spectrum based on precursor ion m/z
... Yes that was the problem, `which(round(precursorMz(rawdata),4)==808.5253)` gave me the index I wanted, thanks! ...
written 3 months ago by garfield32020
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MSnbase extracting individual spectrum based on precursor ion m/z
... Hi, I'm having trouble with extracting individual MS spectrum from my metadata based on precursor ion m/z. rawdata <- readMSData("file.mzXML", msLevel = 2, mode = "onDisk") I'm aware that I can assess individual MS spectrum objects by using index, like `rawdata[[1]]` . But I was tryin ...
msnbase written 3 months ago by garfield32020 • updated 3 months ago by Laurent Gatto1.2k
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Comment: C: MSnbase annotate m/z values on mass spectrum plots
... I initially asked this question because I don't have any sequence information that can be matched to the spectrum, and the code you put as an example (plot(sp, s, main = s)) seemed like it specifically required a sequence-like object for it to work. However, your getting the spectrum into a data fra ...
written 9 months ago by garfield32020
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MSnbase annotate m/z values on mass spectrum plots
... Hi, I'm new to MSnbase package and am trying to plot MS2 spectra with each peaks annotated with their m/z values. I followed the examples from the MSnbase document as below. rawdata <- readMSData("filename", msLevel = 2) sp <- rawdata[which.max(peaksCount(rawdata))] plot(sp, full = TRUE) ...
msnbase written 9 months ago by garfield32020 • updated 9 months ago by Laurent Gatto1.2k

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