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mathiaskalxdorf / IceR

Quantitative proteomics workflow
https://mathiaskalxdorf.github.io/IceR/
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This is mgcv 1.8-40. For overview type 'help("mgcv-package") #24

Open ofleitas opened 2 years ago

ofleitas commented 2 years ago

Hello I am trying to run IceR with the example data and appear work well. However , in certain point of the processing appears this message :

This is mgcv 1.8-40. For overview type 'help("mgcv-package")'. and the processing seem to stall at this point.

Is this normal ?

Best regards

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mathiaskalxdorf commented 2 years ago

Hi, this message is just an information from one of the used packages in the background. As you can otherwise see from the console, this message shows-up after IceR finished its job. R is still running but waiting for your input on the Shiny app (if you would like to start another run or want to have a look at the QC plots of the current run). Best, Mathias

ofleitas commented 2 years ago

Hello

Thank you very much for the help. I was able to reproduce the analyses with the example data. So I tried to perform the analyses with a different data and IceR did the job without problem. But when I tried compare the results of Maxquant with IceR I get the following error

library(IceR)

IceR <- load_Requant_data() [1] "Select Parameters.xlsx" [1] "Selected path to IceR output: C:/Users/ofm83/Documents/anti-virulence/iron/cellular/IceR_results/" [1] "Selected IceR output name: _IceR_analysis" [1] "Selected path to MaxQuant output: C:/Users/ofm83/Documents/anti-virulence/iron/cellular/spectra/combined/txt/" Error in stringr::str_split(data_protein$Gene_Name, ";", simplify = T)[, : subscript out of bounds IceR <- load_Requant_data() [1] "Select Parameters.xlsx" [1] "Selected path to IceR output: C:/Users/ofm83/Documents/anti-virulence/iron/cellular/IceR_results/" [1] "Selected IceR output name: _IceR_analysis" [1] "Selected path to MaxQuant output: C:/Users/ofm83/Documents/anti-virulence/iron/cellular/spectra/combined/txt/" Error in stringr::str_split(data_protein$Gene_Name, ";", simplify = T)[, : subscript out of bounds MaxQ <- load_MaxQ_data() [1] "Select a file in the MaxQ output folder" [1] "Selected path to MaxQuant output: C:\Users\ofm83\Documents\anti-virulence\iron\cellular\spectra\combined\txt\" Error in stringr::str_split(data_protein$Gene.names, ";", simplify = T)[, : subscript out of bounds

Best regards

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