Sentence examples for using the bioconductor suite from inspiring English sources

Statistical analysis was carried out with the data analysis and statistics language R (R Foundation for Statistical Computing) using the Bioconductor suite for bioinformatics59, specifically the limma package57,60 which fits a linear model for each gene and computes a moderated t-statistic and its P value61.

Gene expression data were quantile normalized in R using the Bioconductor suite of software packages.

All calculations were done using the Bioconductor suite in the R software package for statistical analysis [ 4].

Data were reanalyzed using the BioConductor suite in R. We analyzed only probes significantly regulated (fold change > 1.5, p < 0.01) in end-stage M. marinum samples (Dionne et al., 2006).

Microarray data were analysed using the BioConductor suite of packages [ 54] in R. To pre-process the raw expression data, we used the standard RMA (Robust Multichip Average) algorithm [ 55] implemented in the affy package [ 56].

Data were processed using the Bioconductor software suite (Gentleman et al, 2004).

Robust Microarray Analysis (RMA) and Affymetrix Microarray Suite 5.0 (Mas5) background corrections and normalizations were applied independently to the raw data sets using the Bioconductor open source software [51].

Official gene symbols for probe sets were obtained using the Bioconductor annotation database mouse4302.db.

All subsequent analysis was performed using the Bioconductor software environment.

Microarray data were then analyzed using the Bioconductor Limma package.

Calculations were performed using the BioConductor package limma [ 40].