Table 3 Spearman’s correlation coefficients of gene expression levels detected with microarray and RNA-Seq
Data set | Microarray | RNA-Seq platform and pipeline | Gene group | Probes/probe sets (n) | Spearman’s correlation coefficient |
|---|---|---|---|---|---|
NCTR rat TGx | Affymetrix | P2 | A | 8,350 | 0.87 ± 0.02 |
|  | Rat_230_2 |  | B | 7,736 | 0.60 ± 0.04 |
|  |  |  | C | 2,121 | 0.54 ± 0.04 |
SEQC main | Affymetrix | P2 | A | 6,355 | 0.84 ± 0.01 |
|  | HG_U133_Plus 2 |  | B | 27,166 | 0.53 ± 0.02 |
|  |  |  | C | 7,636 | 0.33 ± 0.02 |
SEQC NB | Agilent | P2 | A | 10,042 | 0.73 ± 0.03 |
|  | customized 4 × 44 k |  | B | 13,401 | 056 ± 0.04 |
|  |  |  | C | 2,543 | 0.49 ± 0.04 |
SEQC rat TGx | Affymetrix | P1 | A | 7,829 | 0.88 ± 0.01 |
|  | Rat_230_2 |  | B | 8,376 | 0.63 ± 0.01 |
|  |  |  | C | 95 | 0.64 ± 0.03 |
|  |  | P2 | A | 8,386 | 0.87 ± 0.01 |
|  |  |  | B | 8,035 | 0.68 ± 0.01 |
|  |  |  | C | 3,149 | 0.58 ± 0.01 |
|  |  | P3 | A | 8,201 | 0.89 ± 0.01 |
|  |  |  | B | 8,142 | 0.69 ± 0.01 |
|  |  |  | C | 702 | 0.73 ± 0.01 |
|  |  | P4 | A | 8,080 | 0.88 ± 0.01 |
|  |  |  | B | 8,160 | 0.67 ± 0.01 |
|  |  |  | C | 91 | 0.64 ± 0.04 |
|  |  | P5 | A | 8,197 | 0.85 ± 0.01 |
|  |  |  | B | 7,543 | 0.66 ± 0.01 |
|  |  |  | C | 1,750 | 0.32 ± 0.01 |
|  |  | P6 | A | 5,663 | 0.90 ± 0.01 |
|  |  |  | B | 12,228 | 0.59 ± 0.01 |
|  |  |  | C | 3,189 | 0.38 ± 0.02 |
TCCGA ALM | Affymetrix | Bwa + In | A | 7,448 | 0.82 ± 0.04 |
|  | HG_U133_Plus 2 | House | B | 31,313 | 0.66 ± 0.04 |
|  |  | Program | C | 551 | 0.57 ± 0.04 |