=='''[[User:Lena|Lena Hunt]]'''==

=='''[[User:Lena|Lena Hunt]]'''==

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: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?

:'''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?'''

*There was an off-by-one indexing error in the genes, so they were referencing the wrong genes in the paper.  Furthermore, of the genes in the paper, some worked to split the test set, some worked to split the training set and some worked to explain why the biology worked, but there was no overlap.  Overall, the genes had mislabeled as sensitive or resistance when they were in fact the opposite.  Dr. Baggerly claimed that mixing up sample labels, gene labels, and group labels were common mistakes.

*There was an off-by-one indexing error in the genes, so they were referencing the wrong genes in the paper.  Furthermore, of the genes in the paper, some worked to split the test set, some worked to split the training set and some worked to explain why the biology worked, but there was no overlap.  Overall, the genes had mislabeled as sensitive or resistance when they were in fact the opposite.  Dr. Baggerly claimed that mixing up sample labels, gene labels, and group labels were common mistakes.

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

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

*Dr. Baggerly recommends keeping better records at the research level and labeling published data with a code so that  

*Dr. Baggerly recommends keeping better records at the research level and labeling published data with a code so that  

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