search

broadinstitute / lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project
BSD 3-Clause "New" or "Revised" License
25 stars 13 forks source link

Adding consensus profiles of spherized data #76

Closed gwaybio closed 3 years ago

gwaybio commented 3 years ago

Adding level 5s data to complete @michaelbornholdt 's new-and-improved figure, and close #72

shntnu commented 3 years ago

Quick sanity check: We get the same number of rows with and without spherizing.

From https://github.com/gwaygenomics/lincs-cell-painting/blob/cdcffb04d1a9d8b2b531ab38259e83c82cf7e538/spherized_profiles/generate-consensus-spherized-profiles.ipynb


Now processing batch: 2016_04_01_a549_48hr_batch1
  Now forming consensus signature for: profiles/2016_04_01_a549_48hr_batch1_dmso_spherized_profiles_with_input_normalized_by_dmso.csv.gz
(52223, 1055)
    with consensus operation: median
(10752, 1035)
    Done.
    with consensus operation: modz
(10752, 1035)
    Done.
  Now forming consensus signature for: profiles/2016_04_01_a549_48hr_batch1_dmso_spherized_profiles_with_input_normalized_by_whole_plate.csv.gz
(52223, 830)
    with consensus operation: median
(10752, 810)
    Done.
    with consensus operation: modz
(10752, 810)
    Done.
Batch done.

Now processing batch: 2017_12_05_Batch2
  Now forming consensus signature for: profiles/2017_12_05_Batch2_dmso_spherized_profiles_with_input_normalized_by_dmso.csv.gz
(51447, 763)
    with consensus operation: median
(10368, 741)
    Done.
    with consensus operation: modz
(10368, 741)
    Done.
  Now forming consensus signature for: profiles/2017_12_05_Batch2_dmso_spherized_profiles_with_input_normalized_by_whole_plate.csv.gz
(51447, 557)
    with consensus operation: median
(10368, 535)
    Done.
    with consensus operation: modz
(10368, 535)
    Done.
Batch done.

From https://github.com/broadinstitute/lincs-cell-painting/blob/1769b32c7cef3385ccc4cea7057386e8a1bde39a/consensus/build-consensus-signatures.ipynb


Now processing batch: 2016_04_01_a549_48hr_batch1
  Now Writing: Feature selection: No; Consensus Operation: median; Norm Strategy: whole_plate
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_median.csv.gz
(10752, 1790)
  Now Writing: Feature selection: Yes; Consensus Operation: median; Norm Strategy: whole_plate
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_median_feature_select.csv.gz
(10752, 501)
  Now Writing: Feature selection: No; Consensus Operation: modz; Norm Strategy: whole_plate
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_modz.csv.gz
(10752, 1790)
  Now Writing: Feature selection: Yes; Consensus Operation: modz; Norm Strategy: whole_plate
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_modz_feature_select.csv.gz
(10752, 441)
  Now Writing: Feature selection: No; Consensus Operation: median; Norm Strategy: dmso
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_median_dmso.csv.gz
(10752, 1790)
  Now Writing: Feature selection: Yes; Consensus Operation: median; Norm Strategy: dmso
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_median_feature_select_dmso.csv.gz
(10752, 561)
  Now Writing: Feature selection: No; Consensus Operation: modz; Norm Strategy: dmso
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_modz_dmso.csv.gz
(10752, 1790)
  Now Writing: Feature selection: Yes; Consensus Operation: modz; Norm Strategy: dmso
  File: 2016_04_01_a549_48hr_batch1/2016_04_01_a549_48hr_batch1_consensus_modz_feature_select_dmso.csv.gz
(10752, 496)

Now processing batch: 2017_12_05_Batch2
  Now Writing: Feature selection: No; Consensus Operation: median; Norm Strategy: whole_plate
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_median.csv.gz
(10368, 2207)
  Now Writing: Feature selection: Yes; Consensus Operation: median; Norm Strategy: whole_plate
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_median_feature_select.csv.gz
(10368, 829)
  Now Writing: Feature selection: No; Consensus Operation: modz; Norm Strategy: whole_plate
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_modz.csv.gz
(10368, 2207)
  Now Writing: Feature selection: Yes; Consensus Operation: modz; Norm Strategy: whole_plate
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_modz_feature_select.csv.gz
(10368, 757)
  Now Writing: Feature selection: No; Consensus Operation: median; Norm Strategy: dmso
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_median_dmso.csv.gz
(10368, 2207)
  Now Writing: Feature selection: Yes; Consensus Operation: median; Norm Strategy: dmso
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_median_feature_select_dmso.csv.gz
(10368, 903)
  Now Writing: Feature selection: No; Consensus Operation: modz; Norm Strategy: dmso
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_modz_dmso.csv.gz
(10368, 2207)
  Now Writing: Feature selection: Yes; Consensus Operation: modz; Norm Strategy: dmso
  File: 2017_12_05_Batch2/2017_12_05_Batch2_consensus_modz_feature_select_dmso.csv.gz
(10368, 811)
gwaybio commented 3 years ago

Oh – if possible, please rename the notebooks so that the order is obvious (nice to have)

Will do!