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Table 1 Evaluation of cell-type proportion estimation in bulk samples with known cell type proportions

From: A targeted solution for estimating the cell-type composition of bulk samples

Method

MuSiC

OLS

 

Number of included amplicons

Total

17

18

17

18

CD3

4

5

4

5

CD14

7

7

7

7

CD15

3

3

3

3

CD19

3

3

3

3

 

Correlation with true proportion

CD3

0.990

0.971

0.986

0.954

CD14

0.991

0.988

0.976

0.971

CD15

0.832

0.829

0.796

0.787

CD19

0.742

0.649

0.377

0.358

Mean

0.889

0.859

0.784

0.768

 

Mean cell-type proportion

CD3 (0.28)

0.30

0.27

0.30

0.28

CD14 (0.13)

0.14

0.14

0.16

0.17

CD15 (0.58)

0.52

0.53

0.50

0.51

CD19 (0.08)

0.05

0.05

0.04

0.04

 

Standard deviation of cell-type proportion

CD3 (0.20)

0.22

0.23

0.22

0.23

CD14 (0.03)

0.06

0.07

0.09

0.09

CD15 (0.20)

0.19

0.20

0.20

0.20

CD19 (0.03)

0.05

0.05

0.05

0.05

 

RMSE

CD3

0.042

0.057

0.047

0.067

CD14

0.042

0.048

0.073

0.081

CD15

0.026

0.029

0.049

0.047

CD19

0.040

0.040

0.055

0.057

Mean

0.038

0.044

0.056

0.063

  1. The expected mean and SD are given in parenthesis
  2. OLS is ordinary least square regression