NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data

BMC Bioinformatics

Table 1 Estimated fold change of 10 genes from one sample of simulated dataset2 using NPEBSeq, DESeq and edgeR

gene_ID	9995	9996	9511	9032	9045	9030	9082	3	1
Poisson mean under condition A	0.7741	1.4868	11.5416	424.1334	5.2419	5.2419	112.1307	0.7741	86.6691
Poisson mean under condition B	3.0318	5.8233	45.2038	103.8228	1.2832	1.2832	27.4483	0.758	84.8622
TRUE fold change	4	4	4	4	4	4	4	1	1
observed #reads under condition A	0	0	2	365	34	13	89	0	80
observed #reads under condition B	4	2	37	111	0	1	83	4	72
estimated fc by NPEBSeq	2.5813	1.8077	13.2633	3.3515	18.9702	5.8962	1.1168	2.5813	1.0156
estimated fc by DESeq	inf	inf	18.6932	3.2543	inf	12.8656	1.0612	inf	1.0996
estimated fc by edgeR	60.4244	24.121	58.9655	5.3961	1192.127	29.3642	1.0736	60.4244	1.1299

ISSN: 1471-2105