Difference between revisions of "Class Journal Week 8"

Revision as of 03:56, 18 October 2013

Miles Malefyt

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 main issues with the data and analysis as identified by Baggerly and Coombs were that the end result of the data did not match up with the methods used. The numbers must have been made up or manipulated in many cases in order to get the results which ended up being non-reproduceable.

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

The DataONE and Dr.Baggerly reccomend being consistent with the data used and adhering to the methods described so that they can be reproduceable

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

I feel that much of the scientific community is more oriented towards showing results than making data that is able to be reproduced. It makes me feel like this is more about money and fame than it is about the actual science.

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?

Mmalefyt (talk) 18:44, 17 October 2013 (PDT)

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 genes associated with the particular drugs were incorrect. Their genes were one off in terms of the list, so the set of genes that the research paper described were not actually describing the corresponding biology. Baggerly and Coombs were not able to replicate the data analysis. Some of the common issues that were mentioned is the idea that the easier steps can often be erroneous such as the labeling of genes, sample labels, and group labels, all in all very simple mistakes. The practices that were also violated which is encountered in the DataONE slides was the inconsistency of data and the mislabeling of samples.
2. 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 and as the slides mention, labeling columns are important if charts are used. Also, Dr. Baggerly recommends providing the codes of the analysis.
3. Do you have any further reaction to this case after viewing Dr. Baggerly's talk?
   • It is shocking how the analysis that proved the data to have significant errors were practically ignored, so eventually the clinical trials were permitted. Therefore, the deaths of the cancer patients that took part in this research trial could have been prevented.
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?
   • I don't think there's enough information to reproduce their data analysis. Some of the descriptions are very specific, but some terms are not explained in detail and just mentioned. I was also hoping to see their microarray data by clicking on this provided link http://genome-www5.stanford.edu/microarray/SMD/), but it took me to a "Not Found' page.

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

Lena Hunt

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?