Ozgun Babur, Memorial Sloan Kettering Cancer Center
29 August 2015
Dear authors of CoMEt,
I am having hard time replicating your simulations. There is a mismatch of numbers in your article.
The steps of generating the simulated datasets is given in Additional File 1, section 3. The text says the average number of genes in the simulated datasets (after minimum alteration filtering) is 276. However, when I repeat this procedure, I get an average of 9 genes.
Either the given parameters are wrong, or the average is wrong. You can also see this mismatch without writing any code. The procedure starts with the initial number of genes m=100, and the minimum alteration filtering can only reduce this number. This means the average number of genes has to be equal or less than m.
Can you please clarify this? I need to pass this step to be able to replicate your simulations.
Best,
Ozgun Babur
Competing interests
I am a developer of Mutex
Response to: "A problem in the provided numbers"
Mark Leiserson, Brown University
12 September 2015
Thank you, Ozgun, for pointing out the discrepancy in the number m of genes in the simluations. The number m=100 in the Additional File 1 is a typo. We used m=20,000.
A problem in the provided numbers
29 August 2015
Dear authors of CoMEt,
I am having hard time replicating your simulations. There is a mismatch of numbers in your article.
The steps of generating the simulated datasets is given in Additional File 1, section 3. The text says the average number of genes in the simulated datasets (after minimum alteration filtering) is 276. However, when I repeat this procedure, I get an average of 9 genes.
Either the given parameters are wrong, or the average is wrong. You can also see this mismatch without writing any code. The procedure starts with the initial number of genes m=100, and the minimum alteration filtering can only reduce this number. This means the average number of genes has to be equal or less than m.
Can you please clarify this? I need to pass this step to be able to replicate your simulations.
Best,
Ozgun Babur
Competing interests
I am a developer of MutexResponse to: "A problem in the provided numbers"
12 September 2015
Thank you, Ozgun, for pointing out the discrepancy in the number m of genes in the simluations. The number m=100 in the Additional File 1 is a typo. We used m=20,000.Competing interests
None declared