Error in seq.default(16, nextSBlock - s_indicies[s] - 2, 2)

GarrettLab-UF / LipidMatch

R script using rule based feature identification for lipids

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Error in seq.default(16, nextSBlock - s_indicies[s] - 2, 2) #6

Closed arthuc01 closed 5 years ago

arthuc01 commented 5 years ago

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?

arthuc01 commented 5 years ago

The error was arising because in line 1087

for (m in seq(16, nextSBlock-s_indicies[s]-2, 2)){

because nextSBlock-s_indicies[s]-2) was less than 16, enclosing this for loop in an if statement to check gets it working again

jeremykoelmel commented 5 years ago

Great, feel free to push the change. Usually I just recommend people to use the array filter in MSConvert to remove MS/MS spectra with 2 or less fragments (see manual under Agilent trouble shooting). But this is better if it is fixed in the code. Hope LipidMatch serves you well and sorry for not getting back to you!