gene with FDR < 0.05, is its expression positively or negatively correlated with expression in the microarray experiment ?
What is indicated by FDR is a p-value corrected for multiple testing using the false discovery rate procedure. A p-value represents the probability of seeing the data (or a more extreme version of it) given some hypothesis. It says nothing about the size of the values being measured. If you don't understand p-values and multiple testing corrections, I suggest you read some introduction to statistics.
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version 2.3.6
what?? FDR < 0.05 just shows the gene expression change (up or down regulation) is statistically significant.