Table 5

Symbol

Range

Annotation


dil

1,2,...,G

Number of genes in a dataset with FDR lower than the threshold l

ELg

(0,Inf)

Expected value of the log likelihood with respect to the FDR threshold

fil

1,2,...,dil

Number of false positives using the FDR threshold l

Fgi

(0,1)

Gene-specific false discovery rate in dataset i: proportion of false positives among the significant calls

FDRg

(0,1)

Gene-specific false discovery rate for having consistently differentially expressed patterns among the datasets studied

g

1,2,...,G

Index for a gene from the union of gene sets across all datasets

h

1,2,...,Hi

Index for fold change comparison between a case and a control from a dataset, where mi * ni = Hi

i

1,2,...,D

Index for a gene expression microarray dataset (consists of mi cases and ni controls)

l

(0,1)

FDR threshold used to enumerate number of genes with FDR lower than this threshold in a dataset and to estimate the number of false positives under this threshold

L(rgl|Data)

(0,1)

Gene- and FDR threshold- specific likelihood of observing the differential expressed pattern among the datasets

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1,2,...,G

number of genes that are not up(not down)-regulated in dataset i

Qgl

(0,Inf)

Minus log likelihood

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(0,1)

False positive rate: the probability of a non-up-regulated (non-down-regulated) gene being falsely called as over-expressed (under-expressed)

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0[1]

Binary variable indicating gene g is identified as up(or down)-regulated in dataset i for threshold l

γgih

1,2,...,G

rank of fold change for gene g in the hth comparison of dataset i


Tsoi et al. BMC Bioinformatics 2011 12:438   doi:10.1186/1471-2105-12-438

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