Tinyi Chu

You would need a complete representation for the cell types in your tumor mixture, i.e. including the malignant cells. Please refer to the tutorial and Q&A for the definition of...

Hi. Sorry for the late reply. I am not sure I am quite following. Could you elaborate a bit on the relationship between cell states and tumot/normal state? For example...

Do you mind if sending me a table of cell.type.labels and cell.state.labels (if cell.state.labels differ from cell.type.labels) using something like table(data.frame(cell.type.labels, cell.state.labels)), for both the first round and second round...

When you say "Tumor" and "Normal", do you mean tumor samples and normal samples, rather than malignant and non-malignant cells? I am asking as I saw even lymphocytes show up...

Hi. You may just ignore the warnings. In case it affects anything, please let me know. Thanks.

Thank you for your interest in our method. It might be a good idea to use metacell as cell states, to model the heterogeneity, although we have not tested this....

Hi Alina, Thank you for your interest in our method. The deconvolution module of BayesPrism does not infer any cells unobserved from the reference. For it to work, it is...

Thank you for your interest in our work. Here are the answers to your questions: 1. For my single cell data only cell types information is available. I am not...

Hi Alexandre, Thank you for your interest in our method. Could you do print(bp.res) and head(get.exp(bp.res, state.or.type="type")), and post the results for troubleshooting? Many thanks. Best, Tinyi On Thu, Feb...

Yes. On Fri, Sep 16, 2022 at 3:10 AM weishaoxia ***@***.***> wrote: > I want to deconvolute non-tumor tissue, my cell.type.labels is same with > cell.type.labels, and the "key" of...