has specified data input has specified data output implements has format specification is published by is executed in CEL binary format Propagation of uncertainty in microarray analysis RMA Graph plot puma http://bioconductor.org/packages/2.4/bioc/html/puma.html Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Nandini Badarinarayan BioConductor Software R software CSV data set CEL ASCII format data normalization differential expression analysis Bioconductor