DNA microarray analysis involves a systematic sequence of steps designed to measure the expression levels of thousands of genes simultaneously and to understand global patterns in cellular function. The process begins with the isolation of high-quality RNA from the biological samples being compared, such as diseased versus healthy tissues or treated versus untreated cells. Since microarrays measure gene expression at the transcript level, it is essential that the extracted RNA is intact, free from contaminants, and representative of the cellular transcriptome. The RNA is then converted into complementary DNA (cDNA) or complementary RNA (cRNA) using reverse transcription, often incorporating fluorescently labeled nucleotides to enable later detection. Different samples are typically labeled with distinct fluorescent dyes such as Cy3 and Cy5 to allow comparative hybridization on the same microarray slide. The next step involves preparation of the microarray chip, which