Chapter 3 Cohort Summary Table
3.1 Total number of samples
Firstly, look at the total number of samples:
#recur variables here
avtum=table(Cdata$Rat_ID)
Cchar=Cdata[Cdata$Cohort!="Progression", ]
Cprog=Cdata[Cdata$Cohort=="Progression", ]| Feature | Levels | N |
|---|---|---|
| Total No Tumors | All | 154 |
| - | Characterisation | 66 |
| - | Progression | 84 |
| Total No Rats | All | 84 |
| - | Characterisation | 38 |
| - | Progression | 42 |
| No tumours per rat | 1.83 ( 1, 3) |
3.2 Compare the characterisation vs progression cohort
| Feature | Levels | Characterisation | Progression |
|---|---|---|---|
| Total No tumours | 70 | 88 | |
| Treatments | Vehicle | 62 | 26 |
| - | LY | 18 | |
| - | PDL1 | 17 | |
| - | PDL1+LY | 23 | |
| - | NA | 34 | 4 |
| Histology | diff. adenocarcinomas | 47 | 76 |
| - | mucinous carcinoma | 2 | 3 |
| - | Fibroadenoma | 2 | 4 |
| - | NA | 19 | 5 |
| Age Injection | 32-36 | 22 | 84 |
| - | 35 | 25 | 0 |
| - | 49 | 4 | 0 |
| - | NA | 19 | 4 |
| Time (days) | NMU 2 Sac | 92.09 (55, 160) | 149.37 (79, 248.7) |
| - | Cases with NA | 4 | 4 |
| - | NMU 2 Tumor | 100.62 (44.2, 182.7) | |
| - | Cases with NA | 70 | 4 |
| - | Tum Spec Surv | 48.75 (9.5, 92) | |
| - | Cases with NA | 70 | 4 |
| Growth Rate/Size (mm) | overall size @ sac | 9.83 (2, 20) | 19.52 (3, 40) |
| - | Growing No. | 47 | |
| - | Growing size @ sac | 27.7 15, 28, 40 | |
| - | Stable | 31 | |
| - | Stable size @ sac | 9.58 (1, 6, 24) | |
| - | NA | 70 | 10 |
| Spatial Pattern | |||
| - | Infiltrating | 0 | 26 |
| - | Restricted | 0 | 33 |
| - | NA | 70 | 29 |
| RNA samples | any fraction | 36 | 83 |
| - | Ep | 22 | 21 |
| - | DN | 0 | 33 |
| - | CD45 | 18 | 36 |
| Imaging Data | No tumors | 64 | |
| - | No tumors with RNA | 0 | |
| Trichrome Data | No tumors | 47 | |
| - | No tumors with RNA | 0 | |
| FACS data | Comprehensive | 22 | |
| - | EpCAM/CD45 | 0 | 52 |
3.3 Summary of the RNA data
Below is a table of the samples with RNA information
| Feature | Levels | Characterisation | Progression |
|---|---|---|---|
| RNA samples | any fraction | 0 | 0 |
| - | Ep | 13 | 21 |
| - | DN | 0 | 33 |
| - | CD45 | 10 | 36 |
| Treatments Char/Prev | Vehicle | 13 | 15 |
| - | Untreat (char) | 0 | |
| - | LY | 9 | |
| - | PDL1 | 11 | |
| - | PDL1+LY | 11 | |
| - | NA | 0 | 0 |
| Time | NMU 2 Sac | 102.31 (56.2, 160) | 113.85 (79, 166) |
| Growth Rate/Size (mm) | overall size @ sac | 9.23 (4, 18) | 21.96 (6, 37.5) |
| - | Growing No. | 33 | |
| - | Growing size @ sac | 27.64 15, 28, 40 | |
| - | Stable | 12 | |
| - | Stable size @ sac | 7.17 (3.1, 6, 9.7) | |
| - | NA | 13 | 1 |
| Growth and Treatment: comparing small/stable vs large/growing | |||
| Vehicle | N s/l | 2, 13 | |
| LY | N s/l | 2, 7 | |
| PDL1 and Treatment | N s/l | 4, 6 | |
| PDL1+LY | N s/l | 4, 7 |