The quality of information obtained from microarray experiments is primarily dependent upon the quality of the RNA analyzed. The main factors in isolating good RNA are (1) the composition of the lysis buffer, (2) the method of cell disruption, and (3) the method of separating RNA from proteins. RNA should be devoid of DNA, protein, carbohydrates, and lipids.

Messenger RNA (mRNA), also called transcript, carries the genetic information coded in the genes. Transcript population is diverse. In most cells, transcripts constitute only a small proportion of the total RNA, whereas ribosomal and transfer RNA account for more than 98%. In any cell type, mRNA typically consists of thousands of distinct transcripts, transcribed from different genes. The quantity of transcripts is estimated to follow a normal distribution, of which a small number of genes are expressed at very high or low levels, and the majority are expressed at intermediate levels. Average transcript length is estimated to be between 1.5 – 1.7kb.