The *lumi* package is a Bioconductor package designed specifically for processing Illumina microarray data. It includes data input, quality control, variance stabilization, normalization, and gene annotation. The package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. The *lumi* package provides different normalization methods and multiple quality control plots. To better annotate the Illumina data, a vendor-independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of *lumi* processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data. The *lumi* package includes one major class: LumiBatch, which is inherited from the ExpressionSet class in Bioconductor to enable interoperability with other Bioconductor packages. The class includes numerous methods for preprocessing and quality control. The *lumi* package includes several major processing methods, including *lumiR*, *lumiB*, *lumiT*, *lumiN*, and *lumiQ*, which constitute a preprocessing pipeline. The package also provides different kinds of plot functions for visualization and quality control. The *lumi* package also includes annotation packages that use the nuID to identify the probes of Illumina microarray. The nuID is a loss-less compression of the 50mer oligonucleotide sequence and contains error checking and self-identification code. The *lumi* package provides class infrastructure and associated methods to construct an Illumina analysis workflow pipeline starting with raw data through functional analysis. The package has been improved with comments and contributions from users and researchers worldwide. The current version of the *lumi* package includes methods for data import, quality control, preprocessing, and gene annotation of Illumina microarray data. The package includes several unique parts, including a variance-stabilizing transformation (VST), normalization algorithms, and the nuID annotation packages. The nuID annotation packages allow for version- and vendor-independent annotation of each probe. The nuID also uniquely and exactly encodes the original probe sequence through a process that includes error checking.The *lumi* package is a Bioconductor package designed specifically for processing Illumina microarray data. It includes data input, quality control, variance stabilization, normalization, and gene annotation. The package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. The *lumi* package provides different normalization methods and multiple quality control plots. To better annotate the Illumina data, a vendor-independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of *lumi* processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data. The *lumi* package includes one major class: LumiBatch, which is inherited from the ExpressionSet class in Bioconductor to enable interoperability with other Bioconductor packages. The class includes numerous methods for preprocessing and quality control. The *lumi* package includes several major processing methods, including *lumiR*, *lumiB*, *lumiT*, *lumiN*, and *lumiQ*, which constitute a preprocessing pipeline. The package also provides different kinds of plot functions for visualization and quality control. The *lumi* package also includes annotation packages that use the nuID to identify the probes of Illumina microarray. The nuID is a loss-less compression of the 50mer oligonucleotide sequence and contains error checking and self-identification code. The *lumi* package provides class infrastructure and associated methods to construct an Illumina analysis workflow pipeline starting with raw data through functional analysis. The package has been improved with comments and contributions from users and researchers worldwide. The current version of the *lumi* package includes methods for data import, quality control, preprocessing, and gene annotation of Illumina microarray data. The package includes several unique parts, including a variance-stabilizing transformation (VST), normalization algorithms, and the nuID annotation packages. The nuID annotation packages allow for version- and vendor-independent annotation of each probe. The nuID also uniquely and exactly encodes the original probe sequence through a process that includes error checking.