Dylan Cable

I'm not sure but if you send me the object and script, then I can try reproducing the error. Dylan

Hi, I have tracked the issue down to a problem with small numbers of total counts on these pixels (see attached image below). I have updated the code to throw...

Yes, so now this error indicates that something is wrong. Bead is synonymous with pixel (or spot). The `initial_weight_thresh`, set to .01 by default, is the amount of weight a...

The function `run.CSIDE.replicates` looks for differential expression within each section, for genes that replicate across multiple replicates. For the task you are describing of finding DE genes across replicates, the...

The use of `group_ids` is intended for a different problem: estimating population DE (_within_ samples) when there are multiple samples and multiple replicates within each sample. It does not apply...

Hello, 1. The p_val is unadjusted. We use q_val for the adjusted value. 2. Yes, this is where the FDR test is applied with a q-value threshold. Best, Dylan

Does your code work when using nonparallel mode (1 core)? Let me know if this issue persists after trying @jiawku suggestion.

I think if I'm understanding your question correctly, this functionality can still be handled by the meta regression procedure. If you would like to test for DE across conditions, then...

weight_threshold should be set to at least 75%. This is not the weight of the cell type of interest. It is the total weight of all cell types included in...

Hi Miriam, You can reasonably decrease `cell_type_threshold` to around 25. You can check the amount each cell type appears by using the `count_cell_types` function. If you are missing a cell...