Wet and Dry Lab

The dry lab portion of microarray analyses involves identifying the hybridized spots on the scanned tiff images (gridding) and defining the area and portion of the spot that should be quantified. Most often, mean or median pixel intensities for each spot are extracted from the tiff images. The result is a separate numeric value for each spot and each sample that represents the relative amount of sample hybridized to that spot. Thus, the raw results from an array experiment can be thousands 

The second major goal of the dry lab analyses is to make statistical inferences and discern biological meaning from the expression data. Statistical analyses provide a straightforward approach to analyze microarray data. Genes that are statistically 

The vast amount of data that can result from one microarray experiment has led to analyses incorporating data reduction. Two mechanisms to reduce the data include 

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Figure 3.3. Schematic of a microarray experiment. (A) Experimental design incorporating both biological and technical replication. There are three treated mice and three control mice, providing biological replication. RNA from each mouse is labeled with each dye and hybridized more than once, providing technical replication. The hybridization design uses a loop design as shown in Figure 3.2. (B) Outline of the wet and dry lab steps involved in a microarray experiment. See color insert.

The analysis of a proteome, described as the ensemble of the proteins expressed by a genome in a given tissue, for a given organism at a given time, requires to use and to combine a number of procedures, both experimental (wet-lab experiments) and bioinformatics (dry-lab experiments). Due to the chemical and physical complexity of proteomes, various methodological approaches have to be considered. Nevertheless, a consensus principle of proteome analysis can be described as in Figure 4.1. This linear pathway includes most of the wet- and dry-lab steps required for the complete analysis of a proteome. 

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