XCMS2 on MSMS data
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Titan • 0
@titan-9461
Last seen 3.4 years ago
USA

The problem is highlighted yellow. Trying to run MSMS data file in XCMS. It worked well for the tutorial data and full scan data but did not work for MSMS data. Help please. Problem highlighted in yellow

> list.files()
 [1] "Glycolipids.sld"                                    
 [2] "lipid info.xlsx"                                    
 [3] "Paci772MSMS.RAW"                                    
 [4] "PCFullScanPosIon.RAW"                               
 [5] "PCmw784MSMS.RAW"                                    
 [6] "PEinWeltiPosIonFullScan.RAW"                        
 [7] "PEmw718MSMS.RAW"                                    
 [8] "PEmw740MSMS.RAW"                                    
 [9] "PEmw762MSMS.RAW"                                    
[10] "PGWeltiPosIon.RAW"                                  
[11] "PSmw762MSMS.RAW"                                    
[12] "PSmw784MSMS.RAW"                                    
[13] "PSWeltiPosIon.RAW"                                  
[14] "targeted_positive_lipid1_20121114_Lipid_1_A1_1.mzML"
> library(xcms)
> mzdatafiles <- list.files(pattern="targeted_positive_lipid1_20121114_Lipid_1_A1_1.mzML", recursive = TRUE, full.names = TRUE)
> xraw <- xcmsRaw(mzdatafiles[14], includeMSn = TRUE)
Error in .local(object, ...) : xcmsSource: file not found: NA

Suggestions will be highly appreciated. Naive to the computer world. :)

 

xcms metabolomics massspectrometry lipidomics bioconductor • 1.7k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

What is the length of your mzdatafiles vector? What length do you think it should have? What do you think the 'pattern' argument for list.files() does?

This is very similar to your last question. You are getting an error message that is pretty clear if you read it, but you seem not to be doing so. Let me translate. R is saying 'file not found: NA'. Did you ask it to get a file called NA? R seems to think so. What do you get if you do mzdatafiles[14]?

 

 

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@laurent-gatto-5645
Last seen 3 days ago
Belgium

Your mzdatafiles is a character of length one; it only contains 1 file name, namely "targeted_positive_lipid1_20121114_Lipid_1_A1_1.mzML". Try again with

xraw <- xcmsRaw(mzdatafiles, includeMSn = TRUE)

And by the way, you don't need to use list.files in your case. Just giving the file name is enough

xraw <- xcmsRaw("targeted_positive_lipid1_20121114_Lipid_1_A1_1.mzML", includeMSn = TRUE)

 

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Entering edit mode
Titan • 0
@titan-9461
Last seen 3.4 years ago
USA

Thank you all for your answers.

 

 

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