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waldronlab / BugSigDB

A microbial signatures database
https://bugsigdb.org
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New statistical analysis field: data transformation #154

Closed lgeistlinger closed 1 month ago

lgeistlinger commented 1 year ago

One reviewer raised the following point: There was no indication whether the datasets had been subject to clr-transformation or other compositional data analysis methods. It would be nice to have this as a field or a checkbox since these data are all compositional, but most studies do not adjust for this. I it would be nice to know which are.

After discussion with @lwaldron, we decided that this would be best addressed via a new statistical analysis field called "Data transformation".

  1. This field would be set to NA/blank for all studies already in BugSigDB,
  2. This field would become a field for which we would like control possible values under https://bugsigdb.org/Help:Admin
  3. A user should be able to select from the following options (@lwaldron can you check?):
    • raw counts
    • relative abundances
    • centered log-ratio
    • arcsine
tosfos commented 1 year ago

I assume this will go on the Study form and, therefore, will not vary between Experiments. Please confirm. Also, should this be placed at the end of the form/content page? Or somewhere else?

Please let me know once the final options have been confirmed.

lgeistlinger commented 1 year ago

This will indeed go in the experiment form in the "Statistical analysis" section. It should be the first field, ie before "Statistical test", "Significance threshold", etc.

lwaldron commented 1 year ago

👍 for where @lgeistlinger said.

tosfos commented 1 year ago

Will do. Should we include a tooltip? The other ones have it.

lgeistlinger commented 1 year ago

Yes: "Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any)"

tosfos commented 1 year ago

We implemented this, assuming that you can only have one value in this field. Please let me know if that is incorrect: image

lgeistlinger commented 1 year ago

Looks good, thanks!

lwaldron commented 1 year ago

One minor modification - it should be "arcsine square-root" or "arcsine sqrt" rather than just "arcsine"

tosfos commented 1 year ago

done

cmirzayi commented 1 month ago

Can we add an additional option for "log transformation"? This is different from a central log ratio.

Sorry if there's a way I can add these myself but I couldn't find it.

lgeistlinger commented 1 month ago

Added. Note that autocomplete values can be modified here: https://bugsigdb.org/Help:Admin