When is a Bad Plate Bad?

When running a high-throughput screen, one usually deals with hundreds or even thousands of plates. Due to the vagaries of experiments, some plates will not be ervy good. That is, the data will be of poor quality due to a variety of reasons. Usually we can evaluate various statistical quality metrics to asses which plates […]

Are Bioinformatics Results Too Good To Be True?

I came across an interesting┬ápaper by Ann Boulesteix where she discusses the problem of false positive results being reported in the bioinformatics literature. She highlights two underlying phenomena that lead to this issue – “fishing for significance” and “publication bias”. The former phenomenon is characterized by researchers identifying datasets on which their method works better […]

Viewing Pathways

There are a variety of pathway databases such as KEGG, Reactome and Wikipathways. One of my projects involves pathway analysis, and it’d be nice to easily display them. In many cases, one can simply display a pre-generated image of the pathway (such as in KEGG), but in general, interactivity is nice. However, the latter would […]