Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

BMC Bioinformatics

Table 2 Spearman correlation results of two abundance estimation methods combined with RC and RPKM

Accession	RC	RPKM	RSEM + RC	RSEM + RPKM	Sailfish + RC	Sailfish + RPKM
Reads with length of 35 nucleotides, p-value < 2.2e-16
SRX016359	0.563	0.560	0.690	0.692	0.696	0.694
SRX016366	0.562	0.559	0.689	0.691	0.700	0.695
SRX016367	0.622	0.639	0.755	0.778	0.752	0.797
SRX016368	0.621	0.639	0.755	0.777	0.752	0.797
SRX016369	0.626	0.646	0.770	0.794	0.748	0.806
SRX016370	0.635	0.657	0.778	0.802	0.766	0.815
SRX016371	0.632	0.652	0.773	0.795	0.760	0.811
SRX016372	0.641	0.662	0.781	0.804	0.772	0.819
Reads with length of 76 nucleotides, p-value < 2.2e-16
SRX080222	0.695	0.653	0.691	0.650	0.570	0.583
SRX080223	0.686	0.642	0.682	0.639	0.555	0.575
SRX080224	0.713	0.695	0.711	0.693	0.535	0.602
SRX080225	0.712	0.693	0.709	0.690	0.530	0.597
Simulated-HBR	0.670	0.624	0.667	0.622	0.557	0.579
Simulated-UHR	0.708	0.685	0.705	0.683	0.558	0.629

ISSN: 1471-2105