Dear authors of cellphonedb,
i run the cellphonedb with "cellphonedb method statistical_analysis Rag1_WT_meta.csv Rag1_WT_nondup_exp.csv --output-path=Rag1_WT --counts-data hgnc_symbol --threads 8". And i got the means.txt and deconvoluted.txt files.
But when i check the calculation of mean values for all the interacting partners, i found some results which were not consistent with the "Ducumentation&Results" in the website. there are two cases as following:
the mean value of the interacting pair "TTR_AGER" of "CAF|CAF" (cell types) is 0.124. But, the mean expression of TTR in CAF is 0.0(zero) and the mean expression of AGER in CAF is 0.008.
the mean value of the interacting pair "FGF2_FGFR1" of "CAF|endothelial" (cell types) is 0.156. But, the mean expression of TTR in CAF is 0.298 and the mean expression of AGER in CAF is 0.257.
The description of "mean" in mean.txt is "Mean values for all the interacting partners: mean value refers to the total mean of the individual partner average expression values in the corresponding interacting pairs of cell types. If one of the mean values is 0, then the total mean is set to 0." (https://www.cellphonedb.org/documentation)
it seems that the results are not consistent with the description as mentioned above. (0.298+0.257)/2 != 0.156 , and (0+0.008)/2 should be zero not 0.124.
Bests,
Wenhao
Bouncysig18
commented
1 year ago
Dear authors of cellphonedb, i run the cellphonedb with "cellphonedb method statistical_analysis Rag1_WT_meta.csv Rag1_WT_nondup_exp.csv --output-path=Rag1_WT --counts-data hgnc_symbol --threads 8". And i got the means.txt and deconvoluted.txt files. But when i check the calculation of mean values for all the interacting partners, i found some results which were not consistent with the "Ducumentation&Results" in the website. there are two cases as following: