only treat negative values as missing values for log transformation

[eschen42]

log-transformed data can have meaningful negative values. Issue #7 was applicable only when log-transforming data. Under all other circumstances, negative values must be treated as actual values and not converted to zero.

[eschen42]

Perhaps this is best addressed with a dropdown with two choices (the first as default):

• "Do not alter negative values (e.g., for centered data)"
• "Treat negative values as missing values".

The issue is not really whether data are log-transformed (MS intensities less than one are useless anyway) but rather whether the data are centered. If the tool is expected to respect centered data, then this issue is a bug; otherwise it's an enhancement. I am tentatively removing the bug label.