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zhengrongbin / MEBOCOST

A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
BSD 3-Clause "New" or "Revised" License
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The color that indicates the -log10(FDR) #13

Closed M1chelGom3s closed 7 months ago

M1chelGom3s commented 1 year ago

Dear Dr. Zheng, Thank you for providing MEBOCOST it is very useful to me. I have a problem at the step showing the detailed communications with the mebo_obj.commu_dotmap. The color that indicated the -log10(FDR) is either at max or at minimum. My question is why I am not in between? Thank you in advance.

zhengrongbin commented 1 year ago

Hi - thank you for using MEBOCOST! This means that your FDR values may be very close. You can print the mebo_obj.commu_res to check the actual communication score and FDR values. Also, we use a permutation test to calculate the p-values then convert them to FDR, the more times of permutation (default 1000 times) may give you a more precise p-value calculation, but longer computing takes.

M1chelGom3s commented 1 year ago

Thank you for your response and suggestion. I will definitely check the mebo_obj.commu_res and consider increasing the number of permutations to get a more accurate p-value calculation. I appreciate your help with MEBOCOST.