Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

5.11 MicroRNA Target Prediction Analysis Methods
exonmap package and x:map database [369], to associate microarray probesets
with protein-coding genes annotated in Ensembl 58. Probeset filtering was
applied such that all probe sequences were required to map to exonic gene
components. We estimated the expression level of a gene as the median nor-
malised intensity over its associated probe-sets. Differential gene expression
was computed using the limma package [465], where statistical significance was
determined with a moderated eBayes test and the resulting p-values adjusted
using the FDR method. The microRNA microarray data were background
corrected using the method described by Edwards et al [132] and implemented
in the limma package [465]. Following least-variant set normalization with de-
fault parameters [482], differential expression was computed using the limma
package.
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