gender: male age: eight weeks strain: AJ diet: High Fat High Calorie tissue: liver
Extracted molecule
total RNA
Extraction protocol
standard as recommended by illumina
Label
Biotin
Label protocol
standard as recommended by illumina
Hybridization protocol
standard as recommended by illumina
Scan protocol
standard as recommended by illumina
Description
Male eight weeks AJ strain mouse High Fat High Calorie
Data processing
Raw signal intensities of each probe were obtained using data analysis software(Beadstudio; Illumina) and imported to the Lumi package of Bioconductor fordata transformation and normalization [1-3]. A/P call detection was performed based on detection p value. The probes with less than 0.01 were considered as valid signals. The data for these probes were normalized by quantile method. Differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation [4]. The problem of multiple comparisons was corrected using the false discovery rate (FDR). Initially, genes were identified as being differentially expressed on the basis of a statistically significant (raw p-value < 0.01 and fdr < 0.05 and 1.5-fold change (up or down) in expression level in different treatment samples. [1] Du, P, Kibbe, W. A, and Lin, S. M. (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics. 24(13):1547-8. [2] Lin, S. M., Du, P, Huber, W, and Kibbe, W. A. (2008) Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 36(2):e11 [3] Du, P, Kibbe, W. A., and Lin, S. M. (2007) nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, andother microarrays. Biol Direct. 2:16. [4] Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706.
