I had previously been using Profinder for peak alignment & exporting as a .pfa to use in MPP for further analysis.
We've switched to using Explorer for the alignment piece, and I'm having a problem with the .pfa exported from Explorer.
When I create an MPP experiment with a .pfa from Explorer, I can't really do anything with it - every feature is flagged as Present in every sample (zero Marginal or Absent, even if the abundance is 0), which makes filtering by flags impossible. For example, I try to create an entity list for compounds present in my blanks to subtract them. All Entities is 12,500. No matter what parameter I set (30/30 files, 100%) all 12,500 entities are flagged as Present in the blanks, so it comes out as 12,500 of 12,500. This even happens with samples I know have unique chemicals in them because I spiked them - every sample is 12,500 out of 12,500.
Does Explorer not flag the features like Profinder/MPP does? Is there a setting somewhere in explorer that I can change? Is this a known issue with a workaround or am I just out of luck?
