Table 2 Goodness of fit test for the Poisson and NB models for different protocols from Ziegenhain et al. [12]
From: UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Protocol | Cells Used (n) | Genes tested (n) | Genes reject Poisson (n) | Genes reject NB (n) | Accept Poisson (%) | Reject NB (%) |
|---|---|---|---|---|---|---|
UMI count | ||||||
CEL-Seq2/C1(A) | 30 | 3357 | 660 | 1 | 80.34 | 0.03 |
CEL-Seq2/C1(B) | 33 | 5601 | 1082 | 3 | 80.68 | 0.05 |
Drop-Seq(A) | 37 | 2311 | 548 | 2 | 76.29 | 0.09 |
Drop-Seq(B) | 30 | 1690 | 414 | 0 | 75.50 | 0.00 |
MARS-Seq(A) | 26 | 1162 | 317 | 2 | 72.72 | 0.17 |
MARS-Seq(B) | 32 | 2184 | 750 | 8 | 65.66 | 0.37 |
SCRB-Seq(A) | 35 | 4218 | 214 | 1 | 94.93 | 0.02 |
SCRB-Seq(B) | 40 | 4360 | 213 | 0 | 95.11 | 0.00 |
Read count before converting to UMI | ||||||
CEL-Seq2/C1(A) | 30 | 6012 | 5954 | 622 | 0.96 | 10.35 |
CEL-Seq2/C1(B) | 33 | 7993 | 7897 | 90 | 1.20 | 1.13 |
Drop-Seq(A) | 37 | 4574 | 4386 | 430 | 4.11 | 9.40 |
Drop-Seq(B) | 30 | 2867 | 2781 | 512 | 3.00 | 17.86 |
MARS-Seq(A) | 26 | 2830 | 2743 | 152 | 3.07 | 5.37 |
MARS-Seq(B) | 32 | 4248 | 4168 | 265 | 1.88 | 6.24 |
SCRB-Seq(A) | 35 | 7392 | 7194 | 2065 | 2.68 | 27.94 |
SCRB-Seq(B) | 40 | 7112 | 6855 | 2507 | 3.61 | 35.25 |
Read count | ||||||
Smart-Seq2(A) | 72 | 10,880 | 10,692 | 2696 | 1.73 | 24.78 |
Smart-Seq2(B) | 69 | 10,684 | 10,469 | 1790 | 2.01 | 16.75 |
Smart-Seq/C1(A) | 62 | 9342 | 9249 | 87 | 1.00 | 0.93 |
Smart-Seq/C1(B) | 55 | 7990 | 7893 | 75 | 1.21 | 0.94 |