Table 3. DEG set size and expected PPV of the DEG call methods in the analysis of Rajkumar data set.

Variation in DEG set size and expected PPV were computed using bootstrapping for methods where the DEG set size was not too small or too large.

Method	DEG set size ± SE	PPV∗ ± SE (%)
voom	287 ± 43	88.9 ± 4.1
edgeR	564 ± 694	72.6 ± 15.0
DESeq	3,384	NR
Z-test	9,417	NR
DESeq2	10	NR
NOISeq	31	NR
GFOLD	38	NR

Notes.

SE

standard error

NR

Not Relevant