Data analyses are generally not “one size fits all”; this is particularly true when with approaches used to analyze RNA-seq and microarray data. The characteristics of the data produced by these two technologies can be quite different. This tutorial has example analyses organized by technology so you can follow examples that are more closely tailored to the nature of the data at hand.
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Microarrays measure gene expression using chips filled with oligonucleotide probes designed to hybridize to labeled RNA samples. After hybridization, the microarrays are scanned, and the fluorescence intensity for each probe is measured. The fluorescence intensity indicates the number of labeled fragments bound and therefore the relative quantity of the transcript the probe is designed for.