Because insects elicit gall development by manipulating the plant’s gene expression, many investigators now use modern techniques to determine which genes might be involved. These methods, primarily RNA-sequencing (RNAseq), have provided useful new insights on these unique developmental processes. However, failing to deal with pitfalls in these methods can reduce their utility. In this chapter, we discuss and illustrate some of the problems commonly encountered in assessing and interpreting gall development gene expression using an RNAseq of early gall development driven by grape phylloxera on grape leaves. Results of that experiment indicate that the hostplant synthesizes the phytohormone auxin in response to feeding by phylloxera. Signaling by auxin also appears to happen during early gall stages. These results run counter to the hypothesis that the insect rather than the plant provides auxin to regulate gall development.