The standard method of target synthesis for hybridization to Affymetrix GeneChip® expression microarrays requires a relatively large amount of input total RNA (1-15 micrograms). When small biological samples are collected by microdissection or other methods, amplification techniques are required to provide sufficient target for hybridization to expression arrays. One amplification technique used is to perform two successive rounds of T7-based in vitro transcription. However, the use of random primers required to re-generate cDNA from the first round transcription reaction results in shortened copies of the cDNA, and ultimately the cRNA, transcripts from which the 5' end is missing. In this paper we describe an experiment designed to compare the quality of data obtained from labeling small RNA samples using the Affymetrix Small Sample Target Labeling Protocol V 2 to that of data obtained using the standard protocol. We utilized different preprocessing algorithms to compare the data generated using both labeling methods and present a new algorithm that improves upon existing ones in this setting.