Question

ProFIA package error for noise estimation

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Esther G. • 0

@esther-g-23522

Last seen 3.9 years ago

Hi,

I am attempting to run the R package "ProFIA" however encounter the following error was encountered when I enter this command:

# performing the first step of the workflow ---- 
plasSet <- proFIAset(path, ppm=ppm, parallel=FALSE)

Error message:

Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “logical” is not valid for @‘noiseEstimation’ in an object of class “proFIAset”; is(value, "noiseEstimation") is not TRUE

Does anyone knows how to overcome this?

Below is the link to ProFIA vignette https://bioconductor.org/packages/release/bioc/vignettes/proFIA/inst/doc/proFIA-vignette.html#peak-detection-with-profiaset

Thank you.

Regards, Esther

software error proFIA HRMS FIA Metabolomics • 831 views

ADD COMMENT • link updated 3.9 years ago by Kevin Blighe ★ 3.9k • written 3.9 years ago by Esther G. • 0

Kevin Blighe · Answer 1 · 2020-05-14

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Kevin Blighe ★ 3.9k

@kevin

Last seen 7 days ago

Republic of Ireland

Hey Esther, when I follow the vignette, it works for me:

library(proFIA)
library(plasFIA)
path <- system.file(package="plasFIA", "mzML")
list.files(path)
ppm <- 2
plasSet <- proFIAset(path, ppm=ppm, parallel=FALSE)

Can you show your previous commands and confirm that each has run successfully?

ADD COMMENT • link 3.9 years ago Kevin Blighe ★ 3.9k

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Hi Kevin,

Thanks for your reply. The previous command was ran successfully and the error message occurred after beginning the band detection. I wish to highlight that this occurs when I run my own data files. I have tried their plasFIA package, and I realised it worked well. This is strange as I have the files in the correct format (mzML centroid).

It seems like it could be the input file that has the problem. Would you be able to advise what are the essential information this R package uses from the mzML data to run the noise estimation? Perhaps I can resolve from there. I'm pretty new to R so I was struggling to figure out this information. Many thanks.

Create profile matrix with method 'bin' and step 1 ... OK

Beginning band detection for Data _018



Error in (function (cl, name, valueClass)  :

  assignment of an object of class “logical” is not valid for @‘noiseEstimation’ in an object of class “proFIAset”; is(value, "noiseEstimation") is not TRUE

ADD REPLY • link updated 3.9 years ago by Kevin Blighe ★ 3.9k • written 3.9 years ago by Esther G. • 0

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Unless the actual package developer steps in, I am limited in what I can advise. You have checked the internal structure of your files, I presume, and compared them to the example *.mzML files that come bundled with the package? Also, are you setting noiseEstimation = TRUE?; have you checked the effect of varying the ppm parameter? I worked in mass spec many years ago and recall a lot of variation in the functioning and output between different instruments.

ADD REPLY • link 3.9 years ago Kevin Blighe ★ 3.9k

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I have checked the internal structure of the files and compared to the given mzML files, however not on the effect of varying the ppm parameter. I will give that a try in that case. Thanks!

ADD REPLY • link 3.9 years ago Esther G. • 0