Probe level meta analysis of microarray data to understand the role of retrotransposable elements in myelination.

This study aim to understand the role of retrotransposable elements in myelination Raw data with accession number GSE11218 and GSE5940 (using Affymetrix expresion GeneChIP Rat Genome 230 2.0 and 230A, respectively) were extracted fromm GEO. Probe level information was extracted using R library rat2302probe (for Rat genome 230 2.0) and rae230aprobe (for rat genome 230A). Unique probe sequence in 230 2.0 and 230A platform were retained and the intersect probes (90507 in number) between two platforms were used for analysis. Background subtracted raw data were quantile normalized. Probes for which intensity were greater than. sample median level in at least half the arrays for one experimental condition in. a dataset were considered present; absent probes were removed. Further differentially expressed probbes between OL and OPC were identified by using R Bioconductor package 'limma'. P-values were adjusted to correct for multiple testing using FDR (Benjamini-Hochberg). Probes for which the difference between groups were > or = 2 fold and the adjusted P-value<0.05 were considered differentially expressed. For GSE11218 the samples were: GSM282712, GSM282713, GSM282714, GSM282715, GSM282716, GSM282717, GSM282718, GSM282719. for GSE5940 the samples were: GSM138218, GSM138219, GSM138220, GSM138221, GSM138222, GSM138223, GSM138224, GSM138225, GSM138229