WBPaper00031486:daf-16_upregulated

Raw microarray data (cel files) were normalized, fold-changes between genotypes were determined, and global statistical analysis was performed, using a slightly modified version of the recently described Goldenspike methodology implemented in R (version 2.0.1) (Choe et al. 2005). Briefly, this procedure performs eight different normalization routines, which are then used to produce an average fold-change difference and false-discovery rate (q-value) between different genotypes that takes into consideration the variance of probe set intensity across the different normalizations. The Goldenspike methodology has been shown to out-perform most commonly used normalization methods (Choe et al. 2005). The Goldenspike protocol was altered slightly to exclude absent probe sets (those probe sets called absent in all hybridizations by MAS5) prior to the final probe-set-level Loess normalization. This alteration was found to reduce the number of false positives associated with the absent probe sets (Schuster et al. 2007). Genes showing significantly decreased expression in daf-16(mgDf50);daf-2(e1370) comparing to daf-2(e1370), but not in daf-2(m577).

WBPaper00031486:daf-16_downregulated

Raw microarray data (cel files) were normalized, fold-changes between genotypes were determined, and global statistical analysis was performed, using a slightly modified version of the recently described Goldenspike methodology implemented in R (version 2.0.1) (Choe et al. 2005). Briefly, this procedure performs eight different normalization routines, which are then used to produce an average fold-change difference and false-discovery rate (q-value) between different genotypes that takes into consideration the variance of probe set intensity across the different normalizations. The Goldenspike methodology has been shown to out-perform most commonly used normalization methods (Choe et al. 2005). The Goldenspike protocol was altered slightly to exclude absent probe sets (those probe sets called absent in all hybridizations by MAS5) prior to the final probe-set-level Loess normalization. This alteration was found to reduce the number of false positives associated with the absent probe sets (Schuster et al. 2007). Genes showing significantly decreased expression in daf-16(mgDf50);daf-2(e1370) comparing to daf-2(e1370), but not in daf-2(m577).