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walkthroughs

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n.horner edited this page Apr 22, 2020 · 7 revisions

Download the data

$ lama_get_walkthrough_data # This download test walkthrough data scripts to current directory

Within lama_walkthroughs you should see some shell scripts and a data/ directory

The 3 interactive shell scripts perform various tasks. These can be run from the command line or just opening to get instructions.

  • population_average.sh This creates a population average from 8 male E14.5 WT embryos

  • spatially_normalise_data.sh This script gets the mutant and wild type data registered into the same space as the population average. The script actually uses our E14.5 population average as it has an associated atlas

  • stats_with_BH_correction.sh note: You must run spatailly_normalise_data.sh before running this script

This script run the statistical pipeline comparing the 8 wild types against each mutant line (one line in this case) as we only analyse one line, we apply FDR correction on the pvalues across all the organs (as opposed to across all the lines if we have multiple mutant lines - see [permutation based stats](Permutation based statistics)

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