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closeUnable to replicate results.
Posted by biostem on 24 Feb 2009 at 18:38 GMT
It's impossible to replicate these results because the authors do not supply the source R code they used. The code is not found here or on the website they provided here.
Thank you.
RE: Unable to replicate results because R code is not supplied.
javierdelasrivas replied to biostem on 25 Feb 2009 at 16:37 GMT
Hello,
The paper describes in detail the methods that we used to calculate the two key coefficients used in the construction of the gene coexpression networks: r correlation coefficient (using standard Pearson or Spearman methods) and the N crossvalidation coefficient.
We have used very many small pieces of R and JAVA code to do the work and we have not built a R package or R-BioConductor package because this was not the aim of the work.
The networks can be fully downloaded from PLoS ONE page and our web page (quoted in the paper).
In any case, if some researchers are interested in our R code we could try to build it in an R package.
For any further question, please contact also:
jrivas@usal.es
cprietos@usal.es
RE: RE: Unable to replicate results because R code is not supplied.
biostem replied to javierdelasrivas on 23 Apr 2009 at 20:05 GMT
Thank you for your useful response.
Clearly, is not necessary a "R package or R-BioConductor package". Is sufficient with the R and JAVA code snippets used to generate these results. These code snippets are computational tools with distinct features, and has to be included in the "Methods" section in order to guarantee reproducibility.
The same algorithm implemented in distinct programming language usually gives slightly different results and it's useful to have the original one to reproduce exactly your results and save time.
Regards.