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. 2011 Jun 7;12:228. doi: 10.1186/1471-2105-12-228

Table 5.

A summary of the missing values for each of the tests and the number of significant genes detected by other methods within those missing values.

Significant Genes from Sets of Missing Genes
Method EBA (Affymetrix) Inline graphic (LRT) EBA (RNA-Seq) edgeR DESeq Inline graphic Inline graphic Inline graphic
EBA (Affymetrix) 14292 561 17 589 450 16 2550 1316
Inline graphic (LRT) 75 3979 0 235 197 0 3064 2208
EBA (RNA-Seq) 81 0 4726 235 197 0 3064 2208
edgeR 0 0 0 0 0 0 0 0
DESeq 0 0 0 0 0 0 0 0
Inline graphic 422 973 5 1166 997 8947 4171 2406
Inline graphic 2 0 0 0 0 0 915 0
Inline graphic 3 0 0 0 0 0 856 1832

The diagonal gives the number of genes with missing tests. The off-diagonals indicate those genes that are significant for one method amongst the missing calls for another method. The acronym LRT denotes the likelihood ratio test based on the Poisson distribution, as described in the Methods. The acronym EBA denotes the empirical Bayes analysis performed on both the Affymetrix and RNA-Seq data.