Hi Jeremy and Nick,

I am trying to run the updated script from LipidMatch-3.0.0 but it gets stuck with the following error message (example shown uses the provided example data):

From Directory: \Mac\Home\Desktop\LipidMatch-3.0.0\ExampleData\dd_pos.ms2
Read 564955 items
[1] "Finished Positive by class ddMS analysis"
[1] "Creating Identifications for Positive Mode"
Error in file(file, "rt") : cannot open the connection
Called from: file(file, "rt")

I am aware that this issue has already been raised for the previous LipidMatch version (2.0.2), but I cannot tell whether the current issue is related. I'd be glad if you could have a look at this or give some hints what could be the underlying problem.

I am running R studio (R version 3.3.3) using Windows 10 on my Mac (using Parallels Desktop) and LipidMatch-2.0.2 works fine.

Thank you very much for your help and please keep up your excellent work!

Kind regards,

Albert

Hi,

I made some small changes and I have it running now in R 3.5.1. I also made some changes for selecting folders. This should now work in linux and windows. Unfortunately I have no windows machine to test. If you're interested shall I send you a pull request?

Cheers, Rico

Excuse me,can LipidMatch process data acquired from data independent acquisition (DIA) ,for example ,SWATH mode in an SCIEX 5600 machine?Thank you!

Hello,

I'm running LipidMatch with my own data (positive) ddMS2, the folders: output, ddMS, Pos and PosByClass created are empty.

This is the error message at the end of the running code:
"Read 103055 items
Error in seq.default(16, nextSBlock - s_indicies[s] - 2, 2) :
wrong sign in 'by' argument
Called from: seq.default(16, nextSBlock - s_indicies[s] - 2, 2)"

Someone can help me?

Thank you in advance

Hello, I'm working with Dr. Garrett's lab to run this script on Hipergator (hopefully multi-threaded). Do you by any chance have a version of LipidMatch.r written to run with command line arguments in development? If not I will fork the repo and try to make one, but I don't know much about this tool yet and don't want to reinvent the wheel if not necessary! Thank you.

The code always throws an error when it comes to reading the MS2 files.
Any idea what the issue is?
Cheers,
Thomas
R vers 3.3.3

Reading in file: area_featureTable01_pos.csv
From Directory: C:/R_WorkingDirectory/Sputum_OxLipids/Input/area_featureTable01_pos.csv
Reading in file: CE20_01_ddMS2_pos.ms2
From Directory: C:/R_WorkingDirectory/Sputum_OxLipids/Input/CE20_01_ddMS2_pos.ms2
Read 3872753 items
Error in RunTargeted(MS2_df_in, FeatureList_in, LibraryFile, ParentMZcol_in, :
could not find function "sqldf"

options(warn=0)#suppress warning off

Rversion<-(paste("ERROR:R version must be equal to, or between, 2.0.3 and 3.3.3. Please download 3.3.3. You are using version: ", paste(version$major,version$minor,sep=".")))
OutputRemoval<-paste("ERROR: Remove your 'Output' folder from the current Input Directory: ", InputDirectory)

#DEBUG CreateIDs

ddMS2directory<-"Nothing"

Classdirectory<-"Nothing"

AIFdirectory<-paste(OutputDirectoryAIFPos_in,"Confirmed_Lipids\", sep="")

PeakTableDirectory <- paste(fpath,FeatureTable_POS,sep="")

ddMS2directory <- ddMS2directory

Classdirectory <- Classdirectory

AIFdirectory <- AIFdirectory

ImportLib <- ImportLibPOS

OutputDirectory <- OutputDirectory

ddMS2 <- PosDDLib

ddMS2Class <- PosClassDDLib

AIF <- PosAIFLib

mode <- "Pos"

#CreateIDs(paste(fpath,FeatureTable_POS,sep=""), ddMS2directory, Classdirectory,
#AIFdirectory, ImportLibPOS, OutputDirectory, PosDDLib, PosClassDDLib, PosAIFLib, "Pos")

#Debug AIF

ms1_df<-MS1_df_in

ms2_df<-MS2_df_in

FeatureList<-FeatureList_in

LibraryLipid_self<-LibraryFile

ParentMZcol<-ParentMZcol_in

OutputDirectory<-OutputDirectoryAIFNeg_in

ExtraFileNameInfo<-OutputName

ConfirmORcol<-ConfirmORCol

ConfirmANDcol<-ConfirmANDCol

if(!((as.numeric(paste(version$major,version$minor,sep=""))>=20.3) && (as.numeric(paste(version$major,version$minor,sep=""))<=33.3))) {

• Rversion
• }

if(ErrorOutput==1){

• OutputRemoval
• }

I am running everything using LipidMatch download folder but I kept getting this error message. Any wat to fix it. Thank you.

When I am running lipidMatch using the example dataset and the example library. There come across the following problem:

Error in file(file, "rt") : cannot open the connection

Is there some way to fix it ?

Thank you.

First time user, I'm getting the following error using LipidMatch 2.0.2 under R 3.3.3

Error in seq.default(16, nextSBlock - s_indicies[s] - 2, 2) : 
  wrong sign in 'by' argument

Any suggestions what I might be doing wrong?

Hi, we are trying to run LipidMatch with R 3.3.3 using example data with default parameters (with rowID column = 1, m/z column = 2, rt column = 3, and numeric data row = 2) and get the following output:

[1] "CAUTION: We detected 0 positive AIF .ms1 files in the folder:  ExampleData  ...If this incorrect, check that you have ('AIF') and ('p', 'P', 'pos', or 'POS') at the end of the file name. OR Remove the folder:  ExampleData"
[1] "CAUTION: We detected 0 negative AIF .ms1 files in the folder:  ExampleData  ...If this incorrect, check that you have ('AIF') and ('n', 'N', 'neg', or 'NEG') at the end of the file name. OR Remove the folder:  ExampleData"
[1] "CAUTION: We detected 0 positive AIF .ms2 files in the folder:  ExampleData  ...If this incorrect, check that you have ('AIF') and ('p', 'P', 'pos', or 'POS') at the end of the file name. OR Remove the folder:  ExampleData"
[1] "CAUTION: We detected 0 negative AIF .ms2 files in the folder:  ExampleData  ...If this incorrect, check that you have ('AIF') and ('n', 'N', 'neg', or 'NEG') at the end of the file name. OR Remove the folder:  ExampleData"
Reading in file:	2016_3_11_RC_Plasma_neg.csv
From Directory:		C:\LipidMatch-2.0.2\ExampleData\2016_3_11_RC_Plasma_neg.csv
Reading in file:	dd_neg.ms2
From Directory:		C:\LipidMatch-2.0.2\ExampleData\dd_neg.ms2
Read 326268 items
 Error in match.names(clabs, names(xi)) : 
  names do not match previous names

Can you please help? Seems to be related to an rbind()?

Thank you!