Maren Büttner

Hi Fiona, OK, that sounds reasonably powered overall. Here's what I would adjust in scCODA to improve the FDR: 1. Check the selected reference cell type. Every compositional abundance method...

Hi @Smilenone thank you for your appreciation! On the choice of data normalization as input: When it comes to assessing a batch effect, one essentially wants to understand whether there...

In general, please beware that kBET is probably the most sensitive tool when it comes to batch effects and we realized that the pval may be extremely low even with...

Hi @martina811 thank you for your questions! 1. You can run kBET on the embeddings directly. Internally kBET computes a k-nearest neighbor graph to assess batch effects. 2. You can...

Hi @huawen-poppy thanks for reporting the issue. Do you have a small example to reproduce the error? Happy to help! Thank you!

This also includes the fix suggested in #140

Hi @jesswhitts thanks for pointing this out! A quick fix would be converting all batch codes to numeric values. If your batch covariate is a factor, you can *usually* convert...

Hi @martina811 thank you for pointing out this issue. I tested kBET with batch labels encoded as integers and as factors. My recommendation is that you should use the input...

HI @VishD17 thank you for sharing your results here. The integrated kBET result looks counter-intuitive to me, too. What is the neighborhood size that you use for your data? The...

Hi @wangjiawen2013 thanks for the question! The `kBET` function returns a list of values, one of them is called `results` (see [Usage of kBET function](https://github.com/theislab/kBET#usage-of-the-kbet-function) for details). This contains all...