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Breast cancer classification using limma (Bioconductor)
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    • knitr::opts_chunk$set(fig.align="center", out.width="80%", echo = TRUE)

    Preparations

    Installing packages

    install.packages("tidyverse", quietly=T)
install.packages("gplots", quietly=T)
install.packages("readxl", quietly=T)
install.packages("gplots", quietly=T)
    install.packages("BiocManager", quietly=T)
BiocManager::install("limma", quietly=T, force=TRUE)
BiocManager::install("BiocGenerics", quietly=T, force=TRUE)
BiocManager::install("Biobase", quietly=T, force=TRUE)

    Loading packages

    library("tidyverse", quietly=T)
library("parallel", quietly=T)
library("limma", quietly=T)
library("readxl", quietly=T)
library("BiocGenerics", quietly=T)
library("gplots", quietly=T)
library("Biobase", quietly=T)

    Get data

    url_file <- "https://github.com/friedrfe/breast_cancer_protein_abundance/raw/main/20211212_SubtypeExample.xlsx"
download.file(url_file, "file.xlsx")
    e <- read_xlsx("file.xlsx")

    Exploratory Data Analysis

    head(e)
    glimpse(e)
    summary(e)
    sapply(e, function(x) sum(is.na(x)))
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