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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Finding the differentially expressed genes

At the genome level, the content of every cell is the same, which means that similar genes are present (with a few exceptions) in similar cells. The question that arises then is, what makes cells (for example, control and treated samples) different from one another? This is the question we have most of the time while doing microarray-based experiments. The concept of differential gene expression is the answer to the question. It is well established that only a fraction of a genome is expressed in each cell, and this phenomenon of selective expression of genes based on cell types is the baseline behind the concept of differential gene expression. Thus, it is important to find which genes show differential ...

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