Hi @vonboss, @ShayReza, @LucaChiesa, @jmchap, One question, prompted by what the NTC supplement showed. All 7,703,070 rows of PGK2_selection.parquet have count_PGK2 >= 1 - the minimum is 1, and there are no count_PGK2 = 0 rows. So count_NTC is reported only for compounds detected in the PGK2 arm. Summed over the main file, it is 5,649 reads; adding PGK2_NTC_supplement.parquet brings it to 248,922. The censored subtotal understated that arm by a factor of 44. count_PGK2_with_inhibitor sits in the same file under the same condition, so I assume it is censored the same way, which would make its 49,707-read total a subtotal rather than a depth. 1. Is there a corresponding supplement for the inhibitor arm - compounds with count_PGK2_with_inhibitor >= 1 and count_PGK2 = 0? @vonboss mentioned on 14 Aug having obtained that data from Baylor. Even "not before 1 Oct" would help us plan. 2. If not, could you confirm whether the released inhibitor column is censored to PGK2-positive compounds? That alone changes how the Hit Selection criterion should be read, and it is a one-line answer. For context on why this matters rather than being idle curiosity: fitting the observed inhibitor-to-target read ratio per target-count band on the released file gives 0.0034 at count_PGK2 = 1, rising to 0.38 at counts 101-1000. Since count_PGK2 = 1 covers 98.24% of rows, the recommended count_PGK2_with_inhibitor < 0.1 x count_PGK2 criterion is satisfied for most compounds whether or not competition occurred, while for the few hundred with high target counts it discriminates well. If the column is censored, the low-count end of that curve is partly an artefact. Thanks very much,

Created by Hsuan-Kai Wang DoingWell

Is count_PGK2_with_inhibitor row-censored the same way count_NTC is? page is loading…