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zhengfj1994 / MRM-Ion_Pair_Finder

Defined MRM transitions from untargeted metabolomics data
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error in fun MRM_Ion_Pair_Finder #1

Open stolltho opened 4 years ago

stolltho commented 4 years ago

Hi there.

Executing fun MRM_Ion_Pair_Finder data_ms1ms2_final <- MRM_Ion_Pair_Finder(file_MS1 = "C:\R_WorkingDirectory\MRM_Ion_Pair_Finder\LianneL\Delete Iso-Add Result.csv", filepath_MS2 = "C:\R_WorkingDirectory\MRM_Ion_Pair_Finder\MS2", tol_mz = 0.01, tol_tr = 0.2, diff_MS2MS1 = 13.9, ms2_intensity = 750, resultpath = "C:\R_WorkingDirectory\MRM_Ion_Pair_Finder\LianneL")

returns the following error:

MS1 reading is finished. Read 244910 items Deleting the data in QC_MP_itMS2pos_CE20_it01.mgf with charge > 1 is finished. Error in if (mz_ms1 - mz_ms2 <= diff_MS2MS1 | int_ms2 <= ms2_intensity) { : missing value where TRUE/FALSE needed

Any idea what the problem might be? My r skill level is just basic.

Cheers, Thomas

zhengfj1994 commented 4 years ago

Hi Thomas.

This error is happened when processing the mgf files. If you don't mind, you can send me an example of your mgf file. My e-mail is zhengfj@dicp.ac.cn

Cheers, Fujian Zheng

zhengfj1994 commented 4 years ago

Hi Thomas.

This error is happened because of the format of mgf is different from the mgf file I used. I have modified the code to support your mgf files. In addition, please note that the file name of the mgf files need to be modified to a name that only contains the CE value.

Cheers, Fujian Zheng

stolltho commented 4 years ago

Thanks Fujian. It works now. Cheers, Thomas