Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

Table 1 Numbers of differentially expressed genes called by DESeq using the Workflow 1 generalized linear model. Numbers of genes are listed by analysis factor and normalization method

Factor\Method	TC	UQ	Med	TMM	DESeq^C	Q	RPKM	RC	Overlap
Genotype (G)	10,765	10,110	11,133	11,425	10,464	11,226	8076	5471	4302^A/6372^B
Environment (E)	12,328	8821	10,146	9847	9469	9906	11,737	13,277	5779^A/5819^B
Sex (S)	14,303	14,840	13,042	14,850	14,866	14,515	13,553	14,018	9799^A/10346^B
G x E	3000	3265	1160	3158	3463	3147	896	1318	329^A/483^B
G x S	5942	6926	8441	8084	7163	7703	3414	2659	1771^A/2700^B
E x S	5539	2393	6533	3234	2725	4738	3032	82	62^A/650^B
G x E x S	2492	3410	1889	3501	3611	3767	1018	1202	652^A/900^B

TC total counts, UQ upper quartile, Med median, TMM trimmed mean of M-values, DESeq DESeq normalization method, Q quantile, RPKM reads per kilobase per million mapped, RC un-normalized count data
^A Numbers of overlapping genes among all methods
^B Numbers of overlapping genes among all methods except RC, the un-normalized count data
^CBold indicates preferred normalization method

ISSN: 1471-2164