Method | Annotation | Species | # Common genes | # Differentially expressed genes (% of common genes)a | Spearman’s p valueb | FDR 0.05 | Spearman’s rhob |
---|---|---|---|---|---|---|---|
DESeq2 | Published | D. mau vs D. mel | 11,503 | 2,438 (21.2) | 6.52e-33 | *** | −0.36 |
D. mau vs D. sim | 10,023 | 2,974(29.7) | 2.15e-20 | *** | −0.33 | ||
Direct | D. mau vs D. mel | 13,401 | 2,665 (19.9) | 3.35e-20 | *** | −0.33 | |
D. mau vs D. sim | 13,328 | 3,710 (27.8) | 5.90e-58 | *** | −0.57 | ||
Reciprocal | D. mau vs D. mel | 13,331 | 2,501 (18.8) | 5.12e-02 | n.s. | −0.23 | |
D. mau vs D. sim | 13,320 | 3,508 (26.3) | 1.48e-01 | n.s. | −0.29 | ||
DESeq2 + length matrix | Published | D. mau vs D. mel | 11,503 | 1,192 (10.4) | 2.24e-05 | *** | −0.13 |
D. mau vs D. sim | 10,023 | 1,545 (15.4) | 3.20e-02 | a | −0.08 | ||
Direct | D. mau vs D. mel | 13,401 | 1,259 (9.4) | 1.07e-02 | a | −0.09 | |
D. mau vs D. sim | 13,328 | 1,957 (14.7) | 5.24e-04 | ** | −0.13 | ||
Reciprocal | D. mau vs D. mel | 13,331 | 1,215 (9.1) | 7.03e-01 | n.s. | −4.6e-02 | |
D. mau vs D. sim | 13,320 | 1,910 (14.3) | 7.34e-01 | n.s. | −0.07 | ||
RPKM + limma | Published | D. mau vs D. mel | 11,503 | 1,904 (16.6) | 4.42e-04 | *** | −0.11 |
D. mau vs D. sim | 10,023 | 2,427 (24.2) | 1.06e-03 | ** | −0.12 | ||
Direct | D. mau vs D. mel | 13,401 | 1,890 (14.1) | 5.68e-03 | a | −0.10 | |
D. mau vs D. sim | 13,328 | 2,795 (21,0) | 4.49e-04 | *** | −0.14 | ||
Reciprocal | D. mau vs D. mel | 13,331 | 1,830 (13.7) | 5.92e-01 | n.s. | −6.4e-02 | |
D. mau vs D. sim | 13,320 | 2,738 (20.6) | 2.83e-01 | n.s. | −0.22 | ||
RPKM + voom + limma | Published | D. mau vs D. mel | 11,503 | 1,853(16.1) | 9.39e-04 | *** | −0.10 |
D. mau vs D. sim | 10,023 | 2,204(22.0) | 4.63e-02 | a | −0.07 | ||
Direct | D. mau vs D. mel | 13,401 | 1,899(14.2) | 1.01e-02 | a | −0.10 | |
D. mau vs D. sim | 13,328 | 2,607(19.6) | 5.92e-03 | a | −0.11 | ||
Reciprocal | D. mau vs D. mel | 13,331 | 1,819(13.6) | 5.79e-01 | n.s. | −0.07 | |
D. mau vs D. sim | 13,320 | 2,519(18.9) | 4.06e-01 | n.s. | −0.17 |