Tuesday, November 07, 2006

Long enough to cover the subject, short enough to be interesting.

That was the advice my 10th grade English teacher passed on when asked how much we should produce for a writing assignment. The context (a woman's skirt) he gave was risque enough to get a giggle from 10th graders of the 80's; probably the same joke would get him in serious hot water today -- unless perhaps he pointed out that the same applies for a man's kilt.

A letter in a recent Nature suggests that the same question that vexed me in my student days also bedevils the informatics world. The writer lodges a complaint against MIAME (Minimum Information About a Microarray Experiment), a standard for reporting the experimental context of a microarray experiment. MIAME attempts to capture some key information, such as what the samples are and what was done to them.

The letter writer's complaint is that this is all a fool's mission, as one cannot possibly capture all the key information, especially since what is key to record keeps changing. All reasonable points.

The solution proposed made me re-read the letter for a hint of satire, but I'm afraid they are dead serious.
How should we proceed? Reducing the costs of microarray technology so that experiments can be readily reproduced across laboratories seems a reasonable approach. Relying on minimal standards of annotation such as MIAME seems unreasonable, and should be abandoned.

At first, this just seems like good science. After all, the acid test in science is replication by an independent laboratory.

This utterly ignores two facts. First, by depositing annotated data in central databanks the data can be mined by researchers who don't have access to microarray gear. Second, most interesting microarray experiments involve either specialized manipulations (which only a few labs can do) or very precious limited samples (such as clinical ones); replication would be nice but just can't be done on those same samples.

This "the experiments will be too cheap to database" argument has come up before; I had it sent my way during a seminar in my graduate days. But, like electricity too cheap to meter, it is a tantalizing mirage which fades on close inspection.

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