Preprocessing of Microarray Data

Interpreting the data from a microarray experiment is a challenging task. There are number of sources of systematic variations that affect the measured gene expression levels (Quackenbush, 2002). Such sources of systematic variation include  

This adjusts each ratio such that the mean ratio is equal to 1. An equivalent process is to subtract a constant from the logarithm of the expression ratio (Quackenbush (2002)), 

There are many variations on this particular type of normalization, including scaling the individual intensities so that the mean or median intensities are the same within a single array or across all arrays, or using a selected subset of the arrayed genes rather than the entire collection. 

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