Cluster values

[menage95]

Hello Linnarsson lab,

Thank you for such a great resource!
I have opened your smaller cluster file in python and have sub-setted some of the clusters I am interested in. I was wondering what the numerical value for each cluster/gene meant? are they a normalised value of some sort?

Thanks!
Lucy

[slinnarsson]

They are simple averages of UMI counts, not normalized in any way

[rmd13]

Hello Linnarsson lab,
I am also curious about the normalization in the Genes x clusters: adult_human_20221007.agg.loom.
I opened it in hdfviewer and found a TotalUMI table.
The data in the main matrix table is float with values distributed from 0 to as high as 7. Many of them are 0.000*.
I thought that if a cluster's cell were to be averaged into a number, it is better to normalize the gene level of each cell by the cell's UMI counts, then make an average of all cells inside this clusters. Since UMI counts varies across cells, the cell with lower or higher sequencing depth then will not make the result biased.