Additional file 3.

a table presenting standard differential expression analysis in human data. For each gene (transcript), the results of several two-group comparison tests (carried out with the WGCNA function standardScreeningBinaryTrait) are reported. The first group comparison test contrasts females versus males in control subjects only (columns B through L). The second group comparison test compares controls versus pSS (columns M through W). The third group comparison test compares controls versus sicca (columns × through AH). The fourth group comparison test compares pSS versus sicca (columns AI through AS). Further, columns AT through AZ report the results of a correlation test where each gene was correlated with an ordinal variable that encodes disease status (0 for controls, 1 for sicca, and 2 for pSS). Any column whose name is preceded by corPearson reports the Pearson correlation coefficients where the binary grouping variable (for example, female vs. males) was coded as a binary numeric variable (1 for the first group, 0 for the second group). The meaning of the first and second groups can be learned from column t.Student, which reports the Student t-test statistic. For example, t.Student.F.vs.MGenderInControls shows that the first group corresponds to females and the second group to males (among the control samples). Similarly, t.Student.Control.vs.pSS and t.Student.Control.vs.Sicca show that the first group is comprised of controls. t.Student.pSS.vs.Sicca shows that the first group is comprised of pSS patients. Column meanFirstGroup reports the mean expression value in the first group. FoldChange column reports a signed fold-change value defined by the ratio meanFirstGroup/meanSecondGroup if meanFirstGroup >meanSecondGroup. But if meanFirstGroup <meanSecondGroup, the fold change is defined as minus meanSecondGroup/meanFirstGroup. SE.FirstGroup reports the standard error in the first group. AreaUnderROC reports the area under the receiver operating characteristic curve. pvalueStudent reports the Student t test P value that corresponds to the Student t-test statistic. q.Student reports the corresponding q value (local false discovery rate) calculated with the qvalue R package. nPresentSamples reports the number of nonmissing observations that were available.

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Horvath et al. Arthritis Research & Therapy 2012 14:R238   doi:10.1186/ar4081