1. No category

1.2
1.5
2
3
4
200
8
1
1.2
1.5
2
3
Sample variability
Sample variability
(C)
(D)
4
8
4
8
0.10
0.00
0.00
0.05
0.05
0.10
Empirical FDR
0.15
0.15
0.20
0.20
1
Empirical FDR
150
100
Number of genes detected (FDR<0.1)
150
100
50
0
Number of genes detected (FDR<0.1)
No Weights
Voom
Sample
Voom + Sample
Voom + Block
Sample Removal
250
(B)
200
(A)
1
1.2
1.5
2
3
Sample variability
4
8
1
1.2
1.5
2
3
Sample variability
Supplementary Figure: Boxplot summaries of the number of genes discovered (FDR < 0.1) (A and B) and the
empirical FDR (C and D) for each method across 100 simulated data sets (with 2 groups, n=3 samples per
group) for each of the different sample variability settings explored for the 6th sample. Panels A and C show
results where the simulated true positives have |FC|=2 and B and D where the simulated true positives have
|FC|=4. The results obtained from our new combined weighting methods are similar in variability to other
methods.