1 Sample Information

Analysis from the results of a label free mass spectrometry experiment on paraffin embedded samples stratified as follows:

#Coverage Analysis

On the previously conducted analysis, we could see that filtering the data based on the coverage score was not a good idea as the majority of the proteins had low coverage values. The same analysis was conducted here and the summary statistics of the coverage score for each sample is shown on the table below, and based on that and the plots we can see a similar behaviour regarding the coverage.

## Warning in cbind(stats_1st, summary(coverageDF_1st[[element]])): number of rows
## of result is not a multiple of vector length (arg 2)
First batch of Samples
Fib1 Fib2 Fib3 Fib4 RBC1 RBC2 RBC3
1 3172 4471 3823 0.28000 3120 3254 3305
2 759 1106 907 4.38000 851 907 850
# PSMs 700 952 861 9.52500 616 564 574
3 142 178 139 15.47617 66 90 78
4 52 46 55 21.46000 29 24 29
5 38 19 37 93.88000 11 17 12
7 22 10 14 0.28000 10 6 12
8 14 9 13 4.38000 8 6 9
6 11 9 12 9.52500 4 6 8
10 10 6 11 15.47617 4 5 6
13 4 5 6 21.46000 4 4 6
16 4 5 6 93.88000 4 4 5
21 4 5 6 0.28000 4 4 5
70 4 5 5 4.38000 3 4 4
9 4 4 4 9.52500 3 4 4
0.85 3 4 3 15.47617 3 3 4
1.86 3 4 3 21.46000 3 3 4
11 3 4 3 93.88000 3 3 4
13.68 3 4 3 0.28000 3 3 3
14.29 3 3 3 4.38000 3 3 3
17.65 3 3 3 9.52500 3 3 3
2.18 3 3 3 15.47617 2 3 3
20.51 3 3 3 21.46000 2 3 3
23 3 3 3 93.88000 2 3 3
26.09 3 3 3 0.28000 2 3 3
26.5 3 3 2 4.38000 2 3 3
6.15 3 3 2 9.52500 2 3 2
6.84 3 3 2 15.47617 2 2 2
9.09 3 3 2 21.46000 2 2 2
0.41 2 3 2 93.88000 2 2 2
0.68 2 3 2 0.28000 2 2 2
0.96 2 3 2 4.38000 2 2 2
1.12 2 3 2 9.52500 2 2 2
1.25 2 3 2 15.47617 2 2 2
1.38 2 3 2 21.46000 2 2 2
1.44 2 3 2 93.88000 2 2 2
1.61 2 3 2 0.28000 2 2 2
1.64 2 3 2 4.38000 2 2 2
1.85 2 3 2 9.52500 2 2 2
12 2 3 2 15.47617 2 2 2
12.71 2 3 2 21.46000 2 2 2
13.33 2 3 2 93.88000 2 2 2
14.66 2 3 2 0.28000 2 2 2
14.95 2 3 2 4.38000 2 2 2
15.38 2 3 2 9.52500 2 2 2
16.24 2 2 2 15.47617 2 2 2
16.44 2 2 2 21.46000 2 2 2
17 2 2 2 93.88000 2 2 2
17.09 2 2 2 0.28000 2 2 2
19 2 2 2 4.38000 2 2 2
19.05 2 2 2 9.52500 2 2 2
2.03 2 2 2 15.47617 2 2 2
2.47 2 2 2 21.46000 2 2 2
2.49 2 2 2 93.88000 2 2 2
2.52 2 2 2 0.28000 2 2 2
2.66 2 2 2 4.38000 2 2 2
2.82 2 2 2 9.52500 2 2 2
20 2 2 2 15.47617 2 2 2
21.33 2 2 2 21.46000 2 2 2
21.62 2 2 2 93.88000 2 2 2
22.22 2 2 2 0.28000 2 2 2
23.08 2 2 2 4.38000 2 2 2
24.79 2 2 2 9.52500 2 2 2
26.72 2 2 2 15.47617 2 2 2
28 2 2 2 21.46000 2 2 2
29 2 2 2 93.88000 2 2 2
3.04 2 2 2 0.28000 2 2 2
3.06 2 2 2 4.38000 2 2 2
3.13 2 2 2 9.52500 2 2 2
3.35 2 2 2 15.47617 2 2 2
3.4 2 2 2 21.46000 2 2 2
3.57 2 2 2 93.88000 2 2 2
3.64 2 2 2 0.28000 2 2 2
3.85 2 2 2 4.38000 2 2 2
31.42 2 2 2 9.52500 2 2 2
33.33 2 2 2 15.47617 2 2 2
38.46 2 2 2 21.46000 2 2 2
4.02 2 2 2 93.88000 2 2 2
4.15 2 2 2 0.28000 2 2 2
4.27 2 2 2 4.38000 2 2 2
4.37 2 2 2 9.52500 2 2 2
4.48 2 2 2 15.47617 2 2 2
4.95 2 2 2 21.46000 2 2 2
45.3 2 2 2 93.88000 2 2 2
5.39 2 2 2 0.28000 2 2 2
5.74 2 2 2 4.38000 2 2 2
6.92 2 2 2 9.52500 2 2 2
61.72 2 2 2 15.47617 2 2 2
7.27 2 2 2 21.46000 2 2 2
7.53 2 2 2 93.88000 2 2 2
7.69 2 2 2 0.28000 2 2 2
8.79 2 2 2 4.38000 2 2 2
80 2 2 2 9.52500 2 2 2
9.4 2 2 2 15.47617 2 2 2
9.49 2 2 2 21.46000 2 2 2
9.83 2 2 2 93.88000 2 2 2
0.23 1 2 2 0.28000 2 2 2
0.27 1 2 2 4.38000 2 2 2
0.3 1 2 2 9.52500 2 2 2
(Other) 548 909 737 15.47617 686 732 687
Second batch of Samples
Fib1 Fib2 Fib3 Fib4 Fib5 RBC1 RBC2 RBC3 RBC4 RBC5
Min. 0.18000 0.07000 0.0600 0.28000 0.19000 0.19000 0.04000 0.08000 0.30000 0.13000
1st Qu. 4.73000 4.53500 4.3800 4.38000 4.30000 5.03000 5.01000 4.71000 5.61750 5.02000
Median 10.17000 10.07500 9.9800 9.52500 9.42000 10.94000 11.69000 10.95000 11.06500 10.90000
Mean 15.71651 15.68055 15.3679 15.47617 14.15617 16.54819 15.68757 15.77537 16.03192 15.75879
3rd Qu. 21.55000 23.03000 20.6500 21.46000 19.35000 22.54000 20.87000 21.42250 21.89000 20.62000
Max. 97.28000 91.55000 94.3700 93.88000 94.37000 100.00000 100.00000 100.00000 100.00000 100.00000