Can anyone help me with this code for R code for gene expression? I am stuck on part two of question one where it mentions using limma.?

1. This is in continuation of Question 1 in Homework Assignment 7.

The workflow of microarray data analysis usually follows the steps of

(1) reading in data (often from binary files), (2) normalization, (3)

differential expression detection and (4) generate report. We will

focus on 3 and 4 in this question. We will continue to use the

following packages from Bioconductor: oligo (for reading in data and

normalization), limma and siggenes (for differential expression),

pd.hg.u133.plus.2 (for annotation and generating reports). Refer to

Homework 7 to download the microarray data provided through gene

expression omnibus under accession number GSE18088.

Questions:

(1)How many patients developed relapse events? (5 points)

(2)In order to identify the differential expression genes between

patients with relapse events and patients without relapse, what is

the design matrix for this comparison? (20 points)

(3)Use limma to detect differentially expressed genes between

patients with relapse events and patients without relapse. (35

points)

(4)How many genes are differentially expressed under FDR < 0.05 in

U133Plus2 platform? How many genes with p value < 0.05? What

are the top 30 differentially genes among them? [Hint: use

hgu133plus2SYMBOL to convert Affymetrix probe id to Entrez

gene symbols] (40 points)