biocore/dsfdr

descrete False Discovery Rate method

dsfdr's Issues

using dsFDR on balances

Hi Jamie,

I have not successfully run dsFDR on my gneiss balances yet, but I was wondering what type of output to expect. Will it output which balances pass the FDR test (e.g. y0, y1, y2, etc.), or will it output individual taxa?

If my main interest is individual taxa, would you recommend using dsFDR on "normalized" read counts instead of on balances? Lastly, in your paper on the dsFDR, you mention that counts were normalized. Do you mean they were rarefied to 10,000 reads?

Thanks,
Noah

DS FDR error for Mann-Whitney test

We have followed this workflow for DS- FDR for our data. we have tried to use Mann-Whitney test but their is problem/ error : plugin error from DS-FDR after fixing all bugs. Also we tried to use your example data to test Mann-Whitney test but it gives an error "not enough values to unpack, expected 3 got 2". We have done it using Kruskal-Wallis test but we are unable to apply "Mann-Whitney test " please let us know the suggestions as it is not working on your example data too.
If you can share us your email address that will be better for communication regarding this DS FDR method.

Thanks.
Akshay
[email protected]

dsfdr with method='meandiff' vs. method='mannwhitney'

Hello,
In all examples of dsfdr you used method='meandiff', what is the reason for that? when do we use method='mannwhitney'?
When using method='mannwhitney' I always get reject=False even if it seems it was supposed to be True. Is there a bug in the mannwhitney implementation?
Do we need to shift the data so it will have mean=0 and std=1?
Thanks
Anat

Install has package conflicts

Hello, trying to install in a new conda env and many of the packages have conflicting versions now. Could you specify in the install command? After trying to update everything to versions that don't conflict, I am still unable to use dsfdr and get the error message: ImportError: numpy.core.multiarray failed to import