Class Journal Week 8

Lauren Magee

1. What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?
2. What recommendations does Dr. Baggerly recommend for reproducible research? How do these correspond to what DataONE recommends?
3. Do you have any further reaction to this case after viewing Dr. Baggerly's talk?
4. Look at the methods and results described in the Merrell et al. (2002) paper. Do you think there is sufficient information there to reproduce their data analysis? Why or why not?

Hilda Delgadillo

1. What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?

• The labeling of the drugs were incorrect and two of the most important drugs had been mislabeled. Baggerly and Coombs were not able to replicate the microarrays. Some of the common issues that were mentioned is the idea that the easier steps taken during a microarray analysis is found to be incorrect such as the labeling of genes, sample labels, and group labels, all in all very simple mistakes.

1. What recommendations does Dr. Baggerly recommend for reproducible research? How do these correspond to what DataONE recommends?

He recommends to record everything to avoid incomplete documentation. He recommends labeling as much as possible for graphs as an example. Also, he recommends providing the codes.

1. Do you have any further reaction to this case after viewing Dr. Baggerly's talk?

1. Look at the methods and results described in the Merrell et al. (2002) paper. Do you think there is sufficient information there to reproduce their data analysis? Why or why not?

HDelgadi (talk) 15:58, 17 October 2013 (PDT)