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pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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Gene Ids are not substituted from GeneLookUp #38

Closed ewiger closed 8 years ago

ewiger commented 8 years ago
Module: CreatePlateOverview
Function: generate_basic_data
Project: /BIOL/sonas/biol_uzh_pelkmans_s8/Data/Users/Doris/MOTC_screen_01/20151103_CN_CP611-1aa

Gene Ids are not substituted from GeneLookUp masterdata into the basicdata.mat file.

lookupwellcontent: loading master data from '/cluster/home/biol/yyauhen/iBRAIN_BRUTUS/tools/CellProfilerPelkmans/lib/PelkmansLibrary/matlab/GeneLookup/LookUpGeneData/MasterData.mat'
generate_basic_data: no gene-symbols found in data, normalizing against all wells
generate_basic_data: generating well averages for 15 measurements

To reproduce call:

generate_basic_data('/BIOL/sonas/biol_uzh_pelkmans_s8/Data/Users/Doris/MOTC_screen_01/20151103_CN_CP611-1aa/BATCH/','/BIOL/sonas/biol_uzh_pelkmans_s8/Data/Users/Doris/MOTC_screen_01/20151103_CN_CP611-1aa/P
OSTANALYSIS');

The field BASICDATA.GeneID in the result is empty.

ewiger commented 8 years ago

Deploying and testing this fix on iBRAIN_BRUTUS (switched branch in iBRAIN_BRUTUS/tools/CellProfilerPelkmans/lib/PelkmansLibrary only)

ewiger commented 8 years ago

Fixed has been tested.