Pearson's Correlation Coefficient and expression matrix

1. Microarray analysis

For the following expression data in log2 transformation:

• Calculate Pearson Correlation Coefficient between each pair of genes;
• Calculate the distance matrix as 1 correlation;
• Build a tree based on hierarchical clustering algorithm with average linkage.

2. High-throughput sequencing

Read the attached paper and answer the following questions:

• Explain WGS, Whole-exome and targeted sequencing, RNA-seq, and ChIP-seq;
• Describe three template amplification strategies in few sentences.
• What is single-end sequencing and what is paired-end sequencing?
• What is real-time sequencing?
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2. Build a Pearson correlation matrix for my RNA-seq dataset. My data file consists of normalized, log-transformed expression values of 60k tarnscripts across 50 samples. I want to find the gene-gene Pearson correlation from this matrix using R package or an other tool.