Question: XCMS2 on MSMS data
0
gravatar for Titan
3.6 years ago by
Titan0
USA
Titan0 wrote:

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. :)

 

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Titan0
Answer: XCMS2 on MSMS data
1
gravatar for James W. MacDonald
3.6 years ago by
United States
James W. MacDonald50k wrote:

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]?

 

 

ADD COMMENTlink written 3.6 years ago by James W. MacDonald50k
Answer: XCMS2 on MSMS data
0
gravatar for Laurent Gatto
3.6 years ago by
Laurent Gatto1.2k
Belgium
Laurent Gatto1.2k wrote:

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)

 

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Laurent Gatto1.2k
Answer: XCMS2 on MSMS data
0
gravatar for Titan
3.6 years ago by
Titan0
USA
Titan0 wrote:

Thank you all for your answers.

 

 

ADD COMMENTlink written 3.6 years ago by Titan0
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