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carpenter-singh-lab / 2022_Haghighi_NatureMethods

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
BSD 3-Clause "New" or "Revised" License
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Dataset does not match #9

Open shihanyu opened 1 year ago

shihanyu commented 1 year ago

Hi, I downloaded the dataset with the command aws s3 sync \ --no-sign-request \ s3://cellpainting-gallery/cpg0003-rosetta/broad/workspace/preprocessed_data . And from your application2:
procProf_dir='/home/ubuntu/bucket/projects/2018_04_20_Rosetta/workspace/ metadata_dir='/home/ubuntu/bucket/projects/2018_04_20_Rosetta/workspace/metadata/ but in the dataset downloaded, I only get the preprocessed_data folder, there is no detadata folder. Do I miss something or should I make a empty folder called metadata?

MarziehHaghighi commented 1 year ago

Hi @shihanyu, which script you are trying to run? metadata are added to the preprocessed profiles as extra columns. metadata_dir variable is not used in App1 and App2 scripts. I have deleted the line to avoid the confusion. Sorry for the inconvenience.