I am using arrayQuality and beta7 packages to get an overview of Quality Analysis: > library(arrayQuality) > library(beta7) Loading required package: marray Loading required package: limma > maQualityPlots(beta7) Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' > > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN [4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN [7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beta7_1.0.6 marray_1.40.0 limma_3.18.9 [4] arrayQuality_1.40.0 loaded via a namespace (and not attached): [1] grid_3.0.2 gridBase_0.4-6 hexbin_1.26.3 lattice_0.20-24 [5] RColorBrewer_1.0-5