How is fold change calculated for plotting a comparison between setA versus B in labeled data?

ElucidataInc / ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.

https://resources.elucidata.io/elmaven/

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How is fold change calculated for plotting a comparison between setA versus B in labeled data? #816

Open shefalilathwal opened 6 years ago

shefalilathwal commented 6 years ago

If I have a labeled LC-MS dataset and I am looking at comparison between two sets, how is fold change calculated? Is it from pool totals or intensities of parent or something else?

shubhra-agrawal commented 6 years ago

@shefalilathwal It's the ratio of mean AreaTop intensities of parent. I don't think we use pool totals in El-MAVEN at all at the moment.

chubukov commented 6 years ago

@shefalilathwal @shubhra-agrawal I guess I never tried this, but this feels like not very intuitive behavior -- I would have expected every peakgroup to be included and treated separately.

shubhra-agrawal commented 6 years ago

@chubukov @shefalilathwal I see that the widget does not work very well for labelled data. What would be most useful according to you?

Display every peakgroup separately with an option to "Hide isotopes" to reduce clutter/improve speed
Display every parent group with an option to "Show Pool Totals".

chubukov commented 6 years ago

@shubhra-agrawal (1) seems much more intuitive to me