However, the test still gives a very low P-value of 9.137e−14 when considering the genes with the absolute log moderated fold-changes above 1.
Furthermore, we select a subset of genes with large changes in expression comparing GeneBASE and GeneBASE-xhyb estimates, selected for large absolute log moderated fold-change values, described in Equation (4).
The statistics for differential expression provided by eBayes include the (log) fold change, moderated t-statistic (same as t-statistic except that the standard errors have been moderated across genes), p-value (based on moderated t-statistic), adjusted p-value (false discovery rate adjusted p-value) and B-statistic (log-odds that the gene is differentially expressed).
These filters reduced the dataset to 12,487 genes, of which 1,873 were differentially expressed in ER+ and ER− cancer cell lines, as defined by p<0.05 (FDR q<0.2) from moderated (LIMMA) t-statistics and fold change greater than 1.5.
Differentially expressed genes were identified by fitting a linear model for each gene and evaluating the fold change and moderated t-statistics P-values.
Through the web interface, a user can identify differentially expressed genes by fitting a linear model for each gene and evaluating the fold change and moderated t-statistics P-values (11).
The best parameter for this purpose is signal-to-noise ratio Zd (5) and as it is shown in the paper and Additional file 1 it outperforms ranking by moderated t- test statistics and fold change based methods.
Differential expression was determined by using a combination of moderated t-test p-value and fold change (FC).
For comparison with proteomic data, moderated log-fold changes were calculated using the variance stabilizing transformation supplied by Deseq.
Genes with an absolute moderated t-statistic of > 3.5 and fold change > 2 were considered differentially expressed.
Expression of 22 miRNAs was different between the two groups (p < 0.05 and fold change (FC) > 1.5, moderated t-test, Software "LIMMA").
