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Mesnage-Org / pgfinder

Peptidoglycan MS1 Analysis Tool
https://mesnage-org.github.io/pgfinder
GNU Lesser General Public License v3.0
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Consolidation issue #274

Closed smesnage closed 2 months ago

smesnage commented 2 months ago

Abundance value needs more decimals (currently 2), otherwise consolidation across samples leads to intensities = zero See average tab, highlighted lines in file attached. Cross sample consolidation example.xlsx

TheLostLambda commented 2 months ago

@smesnage Would you like this coupled with multiplying those values by 100 again? Or keep them between 0 and 1, just with more decimals?

It looks like we'd need quite a few... At least 5 decimals if they are between 0 and 1, or up 3 if we're multiplying by 100.

If you could link these raw files here, then we can make sure whatever the number of decimals, that it's enough for this. The other option is just not rounding those numbers at all, and leaving that up to Excel formatting by the user? I don't know if that's a bit too messy though.

Regardless, it's a very easy code change, just let us know what exactly you'd like to see!

smesnage commented 2 months ago

The current consolidation does not give sums that equal 100%. I think this is the thing to check. I think it is better to leave it as a number between 0 and 1 and add 5 decimals. Btw, why not add more?

smesnage commented 2 months ago

Also, another problem (sorry) is that during the consilidation, some intensities that are not equal to zero return a 0% abundance...

image

smesnage commented 2 months ago

file for brooks.xlsx

TheLostLambda commented 2 months ago

No reason not to add more aside from it looking "messy", but these are probably things we really don't want to lose precision on (they need to be non-zero and sum to 1 always!) so I'll just remove the rounding for the abundances!