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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Update Figures 4B/C with only stranded data #1311

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1307

As noted in #1307, there are different sample sizes in Figures 4B and C, but they should have the same samples.

This PR fixes the bug and ensures only stranded data is used for both of these plots. Samples sizes now match. The P-value for the tp53 scores panel has changed since this panel was previously included polya data. It was P=0.23 and now P=0.9, so the overall conclusions are the same. The P-value for the expression panel is the same (P=0.0035) because it was correctly using stranded data only before.

sjspielman commented 2 years ago

Changes do not require CI check. Merging before checks are complete.