vitkl
commented
10 months ago Hi @ssobt
Looks like the main issue is indeed that a sample has many areas have very low counts. I would address that issue rather than figuring out how to input nuclei counts.
- Does nuclei count distribution have a similar distribution to total RNA count? If this is very different it suggests a strong technical effect.
- "Areas with low RNA content have very low probabilities assigned for any of the reference cell types." For areas that have little RNA content, as appears to be the case here, you don't necessarily have enough RNA to distinguish any cell type.
- Including nuclei count into cell2location would not solve the second problem.
- To address, the first problem you could try smaller detection_alpha 0.5 1 2 5. However, if the counts are too low to map anything you would just see noise/similar abundances of all cell types in all low count areas (problem 2).
- In projects that I worked on such as (Madissoon et al, we deleted samples with similarly high variability in total count and large areas of low RNA content.
- You could try deleting all locations with total RNA count < 1000 or a similar cutoff.
Please don't use older versions (cell2location.run_cell2location) because they are not supported and don't correspond to the published paper.
ssobt
huiyijiangling
benoitsam
Hi, thank you for this tool! I have a question about entering in cell counts. I’m using an older version of cell2location (v.02-alpha) to input in nuclei counts for the 'the expected number of cells per location' hyperparamter. We’re having some trouble getting the latest version (v.0.1.3) to assign cell probabilities to most of the tissue due to high RNA variability after trying both 20 and 200 for alpha (see image below for alpha 200). Areas with low RNA content have very low probabilities assigned for any of the reference cell types. To try to alleviate the problem, we switched to the older version to input custom cell/nuclei counts. In v.02-alpha, I have inputted in a 1-dimensional numpy array with the nuclei counts of each spot (made from concatenating rows of 2d x,y array) on the Visium slide, the following error occurs asking for one value instead of locations specific values:
Gamma has no finite default value to use, checked: ('median', 'mean', 'mode'). Pass testval argument or adjust so value is finite.I tried entering the 2d array directly and got the same error. The model only started to run when I entered one integer, so I was wondering how to input nuclei counts per each spot/location? Any advice on this would be great, thanks!
Here is the model setup: