Storey and Tibshirani 2003 method for multitest.multipletests

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Travis Wrightsman

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Jun 28, 2021, 12:16:59 PMJun 28
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Dear statsmodels devs,

I wanted to correct some p-values into q-values according to the algorithm described in Remark B of Storey and Tibshirani 2003 in Python. I didn't find any implementations so I wrote one based off of WGCNA's implementation in R and the paper remark. Is this something that you all would be interested in adding as a new method to multitest.multipletests? I don't see it in the current list of methods but maybe it is very similar to an existing one.

josef...@gmail.com

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Jun 28, 2021, 1:22:48 PMJun 28
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On Mon, Jun 28, 2021 at 12:16 PM Travis Wrightsman <tw...@cornell.edu> wrote:
Dear statsmodels devs,

I wanted to correct some p-values into q-values according to the algorithm described in Remark B of Storey and Tibshirani 2003 in Python. I didn't find any implementations so I wrote one based off of WGCNA's implementation in R and the paper remark. Is this something that you all would be interested in adding as a new method to multitest.multipletests? I don't see it in the current list of methods but maybe it is very similar to an existing one.

We cannot use code that has been based on or is a translation of R code.
The R package is GPL licensed which is not compatible with our BSD license.

I cannot say anything about the method yet. I will have to read up or it. 
Maybe Kerby is familiar with it, he implemented related functions in multipletests.

Josef
 

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Travis Wrightsman

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Jun 28, 2021, 1:45:21 PMJun 28
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I see. It's not a direct translation, but even so it seems like my code
wouldn't be compatible with your license.

Jun 28, 2021 1:22:52 PM josef...@gmail.com:

>
>
> On Mon, Jun 28, 2021 at 12:16 PM Travis Wrightsman <tw...@cornell.edu>
> wrote:
>> Dear statsmodels devs,
>>
>> I wanted to correct some p-values into q-values according to the
>> algorithm described in Remark B of Storey and Tibshirani
>> 2003[https://doi.org/10.1073/pnas.1530509100] in Python. I didn't find
>> any implementations so I wrote one based off of WGCNA's
>> implementation[https://github.com/cran/WGCNA/blob/master/R/qvalue.R]
>> in R and the paper remark. Is this something that you all would be
>> interested in adding as a new method to multitest.multipletests? I
>> don't see it in the current list of methods but maybe it is very
>> similar to an existing one.
>
> We cannot use code that has been based on or is a translation of R
> code.
> The R package is GPL licensed which is not compatible with our BSD
> license.
>
> I cannot say anything about the method yet. I will have to read up or
> it. 
> Maybe Kerby is familiar with it, he implemented related functions in
> multipletests.
>
> Josef
>  
>> --
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>> Groups "pystatsmodels" group.
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