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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

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

Factor\Method TC UQ Med TMM DESeqC Q RPKM RC Overlap
Genotype (G) 10,765 10,110 11,133 11,425 10,464 11,226 8076 5471 4302A/6372B
Environment (E) 12,328 8821 10,146 9847 9469 9906 11,737 13,277 5779A/5819B
Sex (S) 14,303 14,840 13,042 14,850 14,866 14,515 13,553 14,018 9799A/10346B
G x E 3000 3265 1160 3158 3463 3147 896 1318 329A/483B
G x S 5942 6926 8441 8084 7163 7703 3414 2659 1771A/2700B
E x S 5539 2393 6533 3234 2725 4738 3032 82 62A/650B
G x E x S 2492 3410 1889 3501 3611 3767 1018 1202 652A/900B
  1. 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
  2. A Numbers of overlapping genes among all methods
  3. B Numbers of overlapping genes among all methods except RC, the un-normalized count data
  4. CBold indicates preferred normalization method