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counts of gene g at spot s from cell c? #26
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Hello @gorkemkose, I'm glad that you found stereoscope useful! You are correct in your assumption that the However, there might be a solution, what you could do is to compute the expected value for the spots (see: https://en.wikipedia.org/wiki/Negative_binomial_distribution), which would figure as an estimate of the actual x_sgc value. In order to do this, you would need the unadjusted proportions; i.e., the values that are normalized in My suggestion would be for you to either : (1) fork Hope this answered your questions, and lmk how you plan to proceed with this! Best |
Hello again! Sorry for the late reply, I've drowned in the finals and had a short break for the research! This seems exciting, let me try to add the step you have mentioned first. If I can't, will definitely contact you so that maybe you could add this feature when the time permits! Thanks for the support! |
Hi!
Thank you for developing such a nice tool!
I guess the fit_sc_data function returns the parameters that are obtained from SC data's negative binomial distribution. Is this the same thing as r_zg, rate parameter for cell type z and gene g introduced in the paper? Since the method computes counts of gene g at spot s using x_sgc, is there a way we obtain the values of x_sgc, counts of gene g at spot s from cell c as a matrix as well?
Thanks for your time,
Görkem
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