Rub the lamp and make a wish....

A recent article by Allen-Brady , Wong & Camp (2006) in BMC Bioinformatics details a new program called PedGenie which provides a java (GUI) interface to performing association and transmission disequilibrium tests (TDT).

Personally I have mixed feelings about GUI interfaces for analysis, firstly they mean that it is hard to make work reproducible, which is an essential part of any investigation (Gentleman 2005). More importantly because people are often very familiar with point and click interfaces they can go ahead and perform their analysis witout necessarily understanding whether it is appropriate to perform their analysis, or even worse they'll perform every possible test they can and think that because they've found something "significant" they have found an important front. This may come acorss as elitist, but its really not meant to be, since when performing statistical analysis one needs to be very careful and precise about what you are doing.

On the flip side GUI's provide a relatively easy interface to what can be a sometimes impenetrable field, since there is often a steep learning curve to becoming proficent in a given statistical package, OS or scripting language to the extent that one can perform their analysis in a reproducable manner.

At the end of the day its about finding a balance between needing to getting things done, and hey, if it means theres one less person banging on my door needing their hand held to perform their analysis then its not all bad!

References

• Allen-Brady K, Wong J, Camp NJ (2006) PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size BMC Bioinformatics 7:209
  
• Gentlemean R (2005) Reproducible Research: A Bioinformatics Case StudyStatistical Applications in Genetics and Molecular Biology 4:2
  
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