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+,noah,NovaArchSys,29.09.2022 14:42,file:///home/noah/.config/libreoffice/4;
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+# Lab 4 for the University of Tulsa's CS-6643 Bioinformatics Course
+# Differential Expression
+# Professor: Dr. McKinney, Fall 2022
+# Noah L. Schrick - 1492657
+
+## Set Working Directory to file directory - RStudio approach
+setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
+
+#### Part A: Preparing Data
+load("sense.filtered.cpm.Rdata")
+# load phenotype (mdd/hc) data
+subject.attrs <- read.csv("Demographic_symptom.csv", 
+                          stringsAsFactors = FALSE)
+
+if (!require("dplyr")) install.packages("dplyr")
+library(dplyr)
+# grab intersecting X (subject ids) and Diag (Diagnosis) from columns
+phenos.df <- subject.attrs %>% 
+  filter(X %in% colnames(sense.filtered.cpm)) %>%
+  dplyr::select(X, Diag)  
+mddPheno <- as.factor(phenos.df$Diag)  
+
+# Normalized and transform
+library(preprocessCore)
+mddExprData_quantile <- normalize.quantiles(sense.filtered.cpm)
+mddExprData_quantileLog2 <- log2(mddExprData_quantile)
+# attach phenotype names and gene names to data 
+colnames(mddExprData_quantileLog2) <- mddPheno  
+rownames(mddExprData_quantileLog2) <- rownames(sense.filtered.cpm)
+
+length(rownames(sense.filtered.cpm))
+#### Part B: Filter noise genes
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