Sentence examples for using the rma expression from inspiring English sources
Selected arrays were normalized using the RMA expression measure algorithm [ 33].
A clustered heatmap of samples and selected genes was generated using the RMA expression values, uncentered Pearson correlation as a similarity measure and average linkage.
Differentially expressed genes (DEs) among the three stages were selected by multiple testing package multtest [ 40] of R using the RMA expression values.
Selected arrays were normalized according to a three step procedure using the RMA expression measure algorithm (, [ 51]): RMA background correction convolution, median centering of each gene across arrays separately for each data set and quantile normalization of all arrays.
Cluster analysis was performed using the MeV software from the TM4 microarray software suite using the default settings (Euclidean distance, and a maximum of 50 iterations), using the RMA normalized expression values from all 12 samples (3 replicates for each of the four treatments) [60].
Analysis of differentially expressed genes in the different comparisons was performed with the LIMMA package using the RMA normalized expression values [ 66].
The MAQC A and B RNA reference samples were analyzed using the Affymetrix Human Exon 1.0 GeneChips using standard Affymetrix protocols and the data analyzed using the RMA algorithm in the Affymetrix Expression Console software to identify differential expression at the exon level for comparison with the ExpressSeq results[ 29].
Expression data (available at GEO, accession GSE20403) was normalized using the RMA package within the Affymetrix Expression Console software and annotated.
Expression levels were calculated using the rma method [ 19] (implemented in Affymetirx Expression Console tool).
The expression data were summarized on background-corrected and quantile-normalized data using the RMA algorithm implemented in the Affymetrix Expression Console 1.1 software.
Microarray data were normalized and gene expression measures derived using the RMA algorithm, and S-PLUS version 7.0 and SAS version 9.1 were used for the statistical analysis.
