Comments (4)
Hi, I'm running CellPhoneDB with a --result-precision of 10 and I get a lot of straight 0.0 in the p-values output.
I wonder if I should consider them as p<0.0000000001 or if there is another way to look at it?
Like in the Fig5 a of the Single-cell reconstruction of the early maternal–fetal interface in humans paper I would like to plot the results for some clusters and to adjust the size of my dots according to the pvalue, so p-values of zero are a little problematic for me.
Thank you!
from cellphonedb.
Hi,
Yes, that's also what we did to produce the dot plot, we replaced all zeros with very small numbers and then wrote >= certain -log10(p-value) in the legend.
Best,
Mirjana
from cellphonedb.
I am having the same issue. I am using a single cell dataset with ~20k cells, running with the default 1000 permutations, and my p-values with CellPhoneDB are either 0.0 or 1.0. There are a few p-values that are in between, but not many. Is this what one should expect?
from cellphonedb.
Hi,
Please uninstall and then install the new version. --result-precision is now by default 3.
from cellphonedb.
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