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About pyprophet scoring #4808

Open Clovernana opened 4 years ago

Clovernana commented 4 years ago

Hi, When I use the pyprophet to estimate the error rate,the file emerged level didn't show and level features. As is shown in the snapshot,four levels including"ms1","ms2","ms1ms2"and "transition" are not detected.And I used the dataset published as "http://www.peptideatlas.org/PASS/PASS00779" and I just use one part of the data.(that is olgas_K121026_001_SW_Wayne_R1_d00-Mtb_Wayne_01). image

In this case,what should I do next? Thanks so much.By the way,the pyprophet version I used is 2.1.5. Best Wishes.

grosenberger commented 4 years ago

Are you using OSW or TSV input for PyProphet? Only OSW input is compatible with the levels function in PyProphet.

Clovernana commented 4 years ago

yes.

On 7/14/2020 22:32，George Rosenbergernotifications@github.com wrote：

Are you using OSW or TSV input for PyProphet? Only OSW input is compatible with the levels function in PyProphet.

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