User: abrsoule

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abrsoule30
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Posts by abrsoule

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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Yes, I have sent you an email with two species and six corresponding files. ...
written 9 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Good to know about the `x$.self$finalize()` calls. I can send you a few of the files we are working with - I do not htink it is an issue with just one file, as the same error occurs for all of the samples in this project. I can send you all of the samples for three species, as the xcms peak picking ...
written 9 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... We were able to find a temporary fix to the mzR compiling issue and load the newest version of R 3.6.1 and XCMS 3.6.1. However, I am now getting this output after the initial peak picking step: > xcmsexp <- findChromPeaks(object = raw_data, param = cwparam) Detecting mass traces at ...
written 9 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Hi jo, Thanks for the quick response about this issue. I have attempted to update both XCMS and R to their most recent versions (XCMS = 3.6.1, R = 3.6.1) on the linux machine we use for this analysis and found that there is a compiler issue with the mzR package on which XCMS is dependent. According ...
written 9 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... if (length(rtime(z)) != valscantime2) { nrt <- length(rtime(z)) adj_starts_at <- which(rtime(z) == scantime2[1]) adj_ends_at <- which(rtime(z) == scantime2[length(scantime2)]) if ...
written 12 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... rtmaxdiff <- abs(diff(c(scantime1[length(scantime1)], scantime2[length(scantime2)]))) if (rtmaxdiff > (5 * mstdiff)) { rtmax <- min(scantime1[length(scantime1)], scantime2[length(scantime2)]) scantime1 <- scantime1[scan ...
written 12 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... 9: bplapply(objL, function(z, cntr, cntrPr, parms) { message("Aligning ", basename(fileNames(z)), " against ", basename(fileNames(cntr)), " ... ", appendLF = FALSE) suppressMessages(curP <- profMat(z, method = "bin", step = binSize(parms), ...
written 12 weeks ago by abrsoule30
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Comment: C: Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: Bioc
... Using traceback() for the fatal error: 12: stop(.error_bplist(res)) 11: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 10: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) ...
written 12 weeks ago by abrsoule30
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Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6 first error: argument is of length zero
... Hello, I have a large dataset of MS and MSMS data on crude chemical extracts from tropical tree leaves. I have successfully created and run an XCMS pipeline that has allowed us to classify and identify several compounds within these samples that have been run on a 150mm C18 column using reverse pha ...
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mzR unable to open uncorrupted mzXML file
... Hello, I am fairly new to R and to Bioconductor and have been running some code (previously written by another member of our cohort) to analyze our mass spec data. I've run into a couple of issues which I now can't seem to fix. 1) Our peak picking code loops through large numbers of files, nearly ...
xcms mzr software error written 8 months ago by abrsoule30

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