The Importance of Simple Tests in High-Throughput Experiments:
An Adventure with cDNA Microarrays

Keith Baggerly
M.D. Anderson Cancer Center

Abstract:

Microarray expression profiles can provide quick summaries 
of the relative mRNA levels for thousands of genes at once,
and can consequently allow us to ask very sophisticated
biological questions. However, careful processing and 
manipulation of the data is essential, because our intuition
about what the answers ``should look like'' is very poor
when we have to juggle thousands of things at once. Consequently,
simple tests are very important. 

Using a case study done on mice (Pritchard et al, PNAS 2001), 
we describe how one such test questioning the validity of the 
assumption that "most genes don't change" led to a better 
method of normalization for the data set at hand, and how this 
in turn led to the revelation of a more severe problem in data 
organization and sample mixups. We then describe how we were 
able to fix this problem by devising a new test and coupling 
it with the known biology.