{ "cells": [ { "cell_type": "markdown", "id": "f75d5967", "metadata": {}, "source": [ "# Part 1: Exploratory Data Analysis\n", "\n", "In this notebook, we explore the preprocessed datasets generated from my autoimmunity profiling study on Exfoliative Glaucoma (XFG).\n", "\n", "I made three \"slices\" of the data so I can try each one and see which makes the nicest product for this assignment. These are 1) the proteins we found to be significantly different between XFG and controls, 2) group 1 plus 33 random for a total of 40 features, and 3) all 260 antigens included in the study.\n", "I probably will only include group 1, unless these are too easily separable.\n", "\n", "These slices are already preprocessed similar to in the study, including background correction, box-cox transformation, and z-score normalization. If you want the code used for this, I can provide it, but I won't include it here since it's not the focus of this assignment." ] }, { "cell_type": "code", "execution_count": 2, "id": "4ffff549", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Slice 1 (Significant 7) shape: (60, 10)\n", "Slice 2 (Sig 7 + 33 random) shape: (60, 43)\n", "Slice 3 (All proteins) shape: (60, 263)\n" ] }, { "data": { "text/html": [ "
| \n", " | Internal LIMS ID | \n", "Original ID | \n", "group | \n", "HPRA000767 | \n", "HPRA034083 | \n", "HPRA006876 | \n", "HPRA019035 | \n", "HPRA003490 | \n", "HPRA022019 | \n", "HPRA017192 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "GLA_02-0001 | \n", "HD1 | \n", "0 | \n", "0.352329 | \n", "-0.074663 | \n", "0.442451 | \n", "0.210802 | \n", "-0.025678 | \n", "-0.923763 | \n", "0.028253 | \n", "
| 1 | \n", "GLA_02-0002 | \n", "GC1 | \n", "1 | \n", "2.184865 | \n", "0.467075 | \n", "1.272995 | \n", "1.857599 | \n", "2.709290 | \n", "1.367955 | \n", "0.220041 | \n", "
| 2 | \n", "GLA_02-0003 | \n", "HD2 | \n", "0 | \n", "0.519969 | \n", "-0.358698 | \n", "0.124177 | \n", "1.383003 | \n", "1.227493 | \n", "-0.128889 | \n", "-0.343792 | \n", "
| 3 | \n", "GLA_02-0004 | \n", "GC2 | \n", "1 | \n", "1.155189 | \n", "0.467075 | \n", "0.630671 | \n", "0.080847 | \n", "-0.025678 | \n", "-0.416995 | \n", "0.753164 | \n", "
| 4 | \n", "GLA_02-0005 | \n", "HD3 | \n", "0 | \n", "-0.590507 | \n", "-0.074663 | \n", "-1.423605 | \n", "-1.591214 | \n", "-0.375025 | \n", "-0.165849 | \n", "-1.292029 | \n", "