Merge pull request #15 from NIGMS/links-2

Links 2
NIGMS · Nov 15, 2024 · 363455b · 363455b
2 parents 063beb5 + bcc2be1
commit 363455b
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diff --git a/AWS/Module1_proteomic_analysis.ipynb b/AWS/Module1_proteomic_analysis.ipynb
@@ -154,23 +154,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'install' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[4], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# load libraries\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m \u001b[43minstall\u001b[49m\u001b[38;5;241m.\u001b[39mpackages(c(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mreadr\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmatrixStats\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtidyverse\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mggfortify\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mRColorBrewer\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpls\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcolorspace\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdevtools\u001b[39m\u001b[38;5;124m'\u001b[39m))\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'install' is not defined"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# load libraries\n",
     "\n",
@@ -180,9 +166,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "if (!require(\"BiocManager\", quietly = TRUE))\n",
@@ -227,19 +211,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [
-    {
-     "ename": "SyntaxError",
-     "evalue": "invalid syntax (3158474912.py, line 3)",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;36m  Cell \u001b[0;32mIn[3], line 3\u001b[0;36m\u001b[0m\n\u001b[0;31m    devtools::install_github(\"ByrumLab/proteoDA\",\u001b[0m\n\u001b[0m             ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
-     ]
-    }
-   ],
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# proteoDA R package to run proteiNorm functions\n",
     "library(devtools)\n",
@@ -706,7 +679,7 @@
     "### Basic models for covariate and factor explanatory variables.\n",
     "LEFT: The basic model for covariates is referred to as a regression model, which is a line defined by the model parameters β 0 the y-intercept, and β 1 the slope. CENTER: One of two basic models for factors is referred to as a means model, where model parameters are calculated as the mean gene expression of each level of the factor e.g. β 1 represents the mean expression for wildtype and β 2 represents the mean of mutant. RIGHT: The other basic model we refer to for factors is a mean-reference model, where the first model parameter is calculated as the mean gene expression of the reference level, and subsequent parameters are calculated relative to the reference level e.g. β 1 represents the mean expression for wildtype and β 2 represents the difference between mutant and wildtype. In each plot, the points represent the original data; coloured lines are used to represent expected gene expression, where dashed lines are specifically used to represent expected gene expression for non-reference levels in the mean-reference model e.g. mutant.\n",
     "\n",
-    "#### Reference: Charity Law: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873980/#!po=6.25000 "
+    "#### Reference: Charity Law: https://pmc.ncbi.nlm.nih.gov/articles/PMC7873980/ "
    ]
   },
   {
@@ -1100,31 +1073,7 @@
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-   "name": "r-cpu.4-2.m111",
-   "type": "gcloud",
-   "uri": "gcr.io/deeplearning-platform-release/r-cpu.4-2:m111"
-  },
-  "kernelspec": {
-   "display_name": "Python",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
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-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
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+ "metadata": {},
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 }