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some parameters are set to the CSIDE vignette values, which are intended for testing but not proper execution. #179
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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 the model. It just ensures that major cell types are not excluded. You may have to include more cell types in the model that are co-occuring with the cell types of interest. In our paper, we successfully analyzed the dentritic cell cell type which appeared in low proportion (5-10%). The warning message you shared, I am surprised if it would be generated by the parameters included here since none of your parameters match the vignette values. Hope this explanation makes sense. Best, |
Thank you for your response, I have tried to increase the number of cell types but the error complains that the aren't enough cells. So it's asking to remove cell types or decrease
If if I reduce
However if I remove those I get the following:
Apologies for the long post, but I'm still confused about what's the best approach to follow. Thank you very much, Miriam |
Hi Miriam, You can reasonably decrease
If the issue is number 2, then I would recommend looking at the weight matrix of all pixels containing the cell type of interest and seeing which other cell types co-localize. Best, |
Actually, I want to change what I said earlier. This error message is due to not having enough pixels either above or below |
Thank you for your response. I suspect the issue is that I don't have a lot of pixels containing the cells of interest: If I run
|
It looks like of the cell types you mentioned above: All have reasonable cell type counts (>50) except for "Endothelial cells_Vwf high(Lung)". I believe you should be able to get C-SIDE to run using the following cell types: You may have to lower cell_type_threshold a bit. Best, |
Hi,
Thank you very much for developing these great packages. Could you elaborate why the following warning?
Warning message: In run.CSIDE.general(myRCTD, X1, X2, barcodes, cell_types, cell_type_threshold = cell_type_threshold, : run.CSIDE.general: some parameters are set to the CSIDE vignette values, which are intended for testing but not proper execution. For more accurate results, consider using the default parameters to this function.
I have a visium data set, where the cell type of interest seems to have very low weights per spot (around between 5-10%) and in few spots. So in order to
run.CSIDE.single
I have to do:As you can see, the thresholds required for the analysis are way below the defaults. And I was wondering if this is OK to use of what would you advice? Thank you very much for your time and assistance.
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