Minimum Sample Size Unclear

Two patients belong to each group. Looking at the number of cells per sample, I think there are enough cells to test.

2 common reasons ... no cell type has enough cells in >=2 samples per group.

> table(allHumanPairs$samples, allHumanPairs$cellType)
            iCAF mCAF.1 mCAF.2 tpCAF tpCAF..Dividing. Tumor vCAF
  OSCC_16.M    7     95     86  1381              104  2143    0
  OSCC_16.P  588    117     17  1691              501  1185   18
  OSCC_22.M    9      7     15   428              444  1689    0
  OSCC_22.P  263     61      3   818              676  2176   14
  OSCC_24.M    3     23     19   386              267  1687    0
  OSCC_24.P    9    134     16  1430              838  1814    4
  OSCC_60.M    5     30     11   857              248  1654    0
  OSCC_60.P    5     51     10   307              142  3563    0
> table(allHumanPairs$samples, allHumanPairs$Smoker)
              No  Yes
  OSCC_16.M    0 3816
  OSCC_16.P    0 4117
  OSCC_22.M    0 2592
  OSCC_22.P    0 4011
  OSCC_24.M 2385    0
  OSCC_24.P 4245    0
  OSCC_60.M 2805    0
  OSCC_60.P 4078    0

But, all cell types were excluded.

[1] "DE analysis is done:"
[1] "included cell types are:"
NULL
[1] "excluded cell types are:"
[1] "Tumor" "iCAF" "tpCAF" "tpCAF..Dividing." "mCAF.1" "mCAF.2" "vCAF"

saeyslab / multinichenetr

Minimum Sample Size Unclear #94