User: goh

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Posts by goh

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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... Hi, i did try to install xcms 3.3.3 and encounter an error then i use the workaround but still failed to install. So, what im doing now is obtain the xset3 file and from there use the xcms3.2 write.metaboanalyst. > library(devtools) > library(pkgbuild) Attaching package: ‘pkgbuild’ The fol ...
written 12 months ago by goh0
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... Ok, Thanks for pointing our the metlin error. I have another inquiry after i execute the command below. Are we suppose to fillpeaks again ? because in the previous steps i have ran the fillchrompeaks? Looks weird. ## 5_Filling missing peaks using default settings. xdata <- fillChromPeaks(xdata ...
written 13 months ago by goh0
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... Thanks Johannes, it work through. If say i would like to extract the m/z values of certain files, such as 5 from each sample group. What commands need to be added to the command below when i wan to extract the m/z values ? Like filter commands ? mzs <- mz(raw_data) ## Split the list by file m ...
written 13 months ago by goh0
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... I posted the traceback below as well. > traceback() 16: stop(e) 15: value[[3L]](cond) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch({         FUN(...)     }, error = handle_error) 11: withCallingHandlers({         tryCat ...
written 13 months ago by goh0
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... Hi Johannes, I did saw ur recommendations in a few github posts ask ppl to disable parallel processing and tried tht, but another error as below appeared. If i'm not mistaken, it means my RAM ran out of space ? Is there any workaround this ? > register(SerialParam()) > mzs <- mz(raw_data) ...
written 13 months ago by goh0
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Error 'names' attribute must be the same length as the vector xcms
... Hi, I have a total of 50 mzXML ms files (20 treated, 30 un-treated organized into two different subfolders). Then, i have successfully performed LCMS analysis according the the guide huntil when i execute mzs the error as below appeared.   path <- "H:/mzxml" files <- list.files(path, full.n ...
xcms xcms3 mzxml written 13 months ago by goh0
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Does OnDiskMSnExp rewrite original data
... Hi, I'm currently using the new xcms function which executes the following command raw_data <- readMSData(files = cdfs, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk")   The command uses OnDiskMSnExp object from MSnbase Bioconductor package. May i know if i made any changes such as ...
xcms msnbase ondiskmsnexp written 13 months ago by goh0 • updated 13 months ago by Laurent Gatto1.2k

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