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Use SLA for new method #3

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FabRiols opened this issue Dec 1, 2022 · 13 comments
Closed

Use SLA for new method #3

FabRiols opened this issue Dec 1, 2022 · 13 comments

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@FabRiols
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FabRiols commented Dec 1, 2022

Hello,
I would like to use the SLA for a new and independent DMS method, for Cardiolipins.
The method is totally independent of the "Lipidyzer-like" method, for instance I only have negative mode acquisition.
I've modified the information in the Tuning_Spname_dict to get SST intensities, but I couldn't make it work.
Here is the error message: IndexError: ('index 0 is out of bounds for axis 0 with size 0', 'occurred at index 0')
I wonder if it could come from the fact that I don't have neg and pos mode for the acquisition method.
It would be great to get some help!
Thank you a lot.

Bets wishes,
Fabien
@syjgino
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syjgino commented Dec 1, 2022 via email •
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@FabRiols
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FabRiols commented Dec 2, 2022 via email •
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@syjgino
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syjgino commented Dec 2, 2022 via email

@FabRiols
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FabRiols commented Dec 9, 2022

I've tested the analysis of the 3 methods and it works with the SLA, that's so great!
Just one issue, the output_merge.xlsx file does not contain the results of the method 03. I've taken a look at your code and indeed it seems that the method 03 was not implemented in the "merge m1 m2 m3 dataframes" section.
Would it be please possible to get a new version of the SLA with the m3 merging?
Thank you so much :)
Best,
Fabien

@FabRiols
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FabRiols commented Dec 9, 2022

Also, the isotope correction for method 03 doesn't work. Indeed the SLA doesn't read the sheat 'M3' as you can see below:
"

read iso correction dict

if variable_iso.get() == 'Yes':
    iso_dict = {'1': pd.read_excel(iso_dict_loc.get('1.0', 'end-1c'),
                                   sheet_name='M1', header=0, index_col=None, na_values='.'),
                '2': pd.read_excel(iso_dict_loc.get('1.0', 'end-1c'),
                                   sheet_name='M2', header=0, index_col=None, na_values='.')}

##reading mzml loop start
"

@syjgino
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syjgino commented Dec 9, 2022 via email •
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@FabRiols
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Hi Gino,

Thank you for all the explanation.
I've generated the method 3 files as "method 3" so according to your code I guess I cannot apply them as method 01 as I cannot modify file names within mzml data files.
So I'm really looking forward to this source code update.
Thanks a lot.

@syjgino
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syjgino commented Dec 12, 2022 via email

@FabRiols
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I can see in SRC that the file was updated, thank you, but I don't know how to use it - I never used Python before: isn't necessary to generate a new version of the SLA?

@syjgino
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syjgino commented Dec 14, 2022 via email

@FabRiols
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I did as you said and it works, but without isotope correction. It seems then that there is an issue in my ISOcorrectlist_V3_3.0 file and the software stops at line 137 in isoadjv2.
I've built the sheet as the others and according to your SOP so I don't know where is the problem.

@syjgino
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syjgino commented Dec 16, 2022 via email

@FabRiols
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FabRiols commented Jan 4, 2023 •
edited

Yes the sheet was named M1. I finally found the error, ISTDs were not assigned as such in the ISOcorrectlist (forgot the "d" before the compound name). Works great now. Thanks!

@syjgino syjgino closed this as completed Jan 11, 2023
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@syjgino @FabRiols