Class Journal Week 8

Zachary Van Ysseldyk's Responses

1. The main issues with the data and analysis identified was that the data was not reproducible - actually, that the data was very very far from reproducible. They reused the same genes in statistical analysis, their indexing was off by one, and some of their verification tables (namely the 59 gene ovarian cancer model) matched 0% of what the line was supposed to be. Based on his overall observations, he says the most common mistakes are simple. He says how this simplicity is often hidden, and furthers to say that the most simple mistakes are common. Specifically, he found the most common mistakes concerning: Mixing up sample labels, Mixing up the gene labels, Mixing up the group labels, and incomplete documentation. He notes how the MOST common mistake is the complete confounding in the Experimental design.
2. Baggerly first suggests that the data should be labeled in order to clearly be able to tell which data is which.