WHOIGit / domdb

DOM mass spec database prototype
MIT License
1 stars 3 forks source link

Zero-like intensities in output. A problem? #26

Closed joefutrelle closed 9 years ago

joefutrelle commented 9 years ago

I'm seeing intensities with a value of 0E-10 in match output. Here's an example from DeepDOM traps. Are these zero-like intensities expected? Should they be included in the output of search and all? If so then there's no problem.

(Cmd) search 678.4175 830
Found 1 matches
mtab_exp,mtab_mz,mtab_rt,match_exp,match_mz,match_rt,sample,intensity,control,ignore,SampleType,Station,Date,station,sampleType,control_1,ignore_1
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_48,65380.3089725788,0,0,TrapSample,12,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_47,8393.4329264963,0,0,TrapSample,15,4/25/2013,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_45,13052.6320985002,0,0,TrapSample,16,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_44,0E-10,0,0,TrapSample,23,7/1/2013,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_43,80900.5575851031,0,0,TrapSample,21,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_41,8501.3258026857,0,0,TrapSample,23,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_40,300.4008678827,0,1,TrapSample,22,,,QC,0,0
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_46,296863.2116549130,0,0,TrapSample,5,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_38,19857.8392084213,0,0,TrapSample,9,,Bio9,PPL,0,0
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_39,0E-10,0,1,TrapSample,11,,,blank,0,0
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_54,1998.3955365916,0,0,TrapSample,19,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_55,0E-10,0,0,TrapSample,7,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_56,405.3706954574,0,0,TrapSample,15,4/22/2013,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_57,0E-10,0,0,TrapSample,15,7/1/2013,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_58,462.3691755587,0,0,TrapSample,18,,,,,
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_36,795.9297520717,0,0,TrapSample,15,4/30/2018,seawater,PPL,0,0
N/A,678.4175,830.0,deep,678.4175413963,832.1574000000,mtab_TrapFilters_FT_37,26349.1375322516,0,0,TrapSample,32,,CrabSpa,PPL,0,0
redbluewater commented 9 years ago

This seems to be a data input error. In the CSV files I have, they are shown as 0. I went through the data in the query above and all the cases where there is 0e-10 are 0 in the CSV file. These should be 0 (and hence ignored in the query). However, I am more curious as to why they are being converted to 0e-10.

joefutrelle commented 9 years ago

I'm pretty sure the "0e-10" is just an output formatting quirk, and the underlying bug is that there are some zero intensities that I'm not excluding properly during ETL.