Skip to main content
Premium Trial:

Request an Annual Quote

Statisticians Advice: How to Do a Microarray Experiment Well

Premium

At last week’s Microarray Data Analysis conference in Washington D.C., several speakers laid out what distinguishes a good microarray experiment from a bad one. Here is their collected advice:

• Consult a statistician before you even design your experiment. They have more to offer than just analysis tools.

• Formulate your hypothesis, even if you are going on a “fishing expedition.” What is the question you want to answer?

• Do a power analysis to determine the number of replicates (i.e. chips) you need to detect an effect. To estimate the effect size, you might want to run a pilot study first or obtain the estimate from previous similar experiments. Regardless of the power analysis results, obtain at least three replicates on different slides or chips.

• Find sources of technical variation before you embark on a hunt for biological effects. Some common sources are: target preparation and chip processing, day or time of day of the experiment, location, chip lots, scan order, or the researcher running the experiment.

• Standardize your protocols as much as possible, and train your technicians until they obtain consistent results.

• Randomize your variables: for example, don’t run all your treatment slides on one day and all your controls on the next; stagger chip lots across experiments if you need to.

• Choose the appropriate statistical tool for your analysis. Cluster analysis cannot answer all the questions.

The Scan

Fertility Fraud Found

Consumer genetic testing has uncovered cases of fertility fraud that are leading to lawsuits, according to USA Today.

Ties Between Vigorous Exercise, ALS in Genetically At-Risk People

Regular strenuous exercise could contribute to motor neuron disease development among those already at genetic risk, Sky News reports.

Test Warning

The Guardian writes that the US regulators have warned against using a rapid COVID-19 test that is a key part of mass testing in the UK.

Science Papers Examine Feedback Mechanism Affecting Xist, Continuous Health Monitoring for Precision Medicine

In Science this week: analysis of cis confinement of the X-inactive specific transcript, and more.