Hi,
I am using CellphoneDB for my research project and have several questions about the output files and their potential interpretations.
In the p-values.txt file, I notice that many cell type interactions have a p-value of 0 or 1. For those with a value of zero, should I interpret them as interactions with higher significance since they are less than 0.05? For those with p-values of 1, should I consider them as not significant because they are greater than 0.05?
According to the online documentation, I should focus on specific cell type pairs and manually review interactions, prioritizing those with a lower p-value and/or higher mean expression. Do you recommend using any specific lower threshold for the mean expression value?
Regarding the significant_means.txt file, can you please explain how to interpret the results? The documentation states that if the p-value < 0.05, the value will be the mean; otherwise, the value is set to 0. (Only in significant_means.txt). However, in my output, many cells are blank and contain no values. I am unsure how to interpret this, and any advice would be greatly appreciated.
Thank you very much for your help!
Best regards,
Ankita Samanta
Hi,
I am using CellphoneDB for my research project and have several questions about the output files and their potential interpretations.
In the p-values.txt file, I notice that many cell type interactions have a p-value of 0 or 1. For those with a value of zero, should I interpret them as interactions with higher significance since they are less than 0.05? For those with p-values of 1, should I consider them as not significant because they are greater than 0.05?
According to the online documentation, I should focus on specific cell type pairs and manually review interactions, prioritizing those with a lower p-value and/or higher mean expression. Do you recommend using any specific lower threshold for the mean expression value?
Regarding the significant_means.txt file, can you please explain how to interpret the results? The documentation states that if the p-value < 0.05, the value will be the mean; otherwise, the value is set to 0. (Only in significant_means.txt). However, in my output, many cells are blank and contain no values. I am unsure how to interpret this, and any advice would be greatly appreciated.
Thank you very much for your help!
Best regards,
Ankita Samanta