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 features a variance-stabilizing transformation (VST) algorithm that utilizes technical replicates available on Illumina microarrays. It also provides multiple normalization methods and quality control plots. A vendor-independent nucleotide universal identifier (nuID) was developed to uniquely identify Illumina probes, enabling version- and vendor-independent annotation. The nuID allows for accurate encoding of probe sequences and error checking. The lumi package is built upon the ExpressionSet class in Bioconductor, enabling interoperability with other Bioconductor packages. It includes a LumiBatch class that holds data, control probe information, and quality control summaries. The package includes methods for preprocessing and quality control, such as lumiR, lumiB, lumiT, lumiN, and lumiQ, which together form a preprocessing pipeline. A lumiExpresso method encapsulates all four methods into one. The package also provides various plot functions for visualization and quality control. The annotation packages in lumi use nuID as the identifier for probes, allowing for version- and vendor-independent annotation. These packages can be downloaded from Bioconductor and are designed for different Illumina expression chips. The lumi package enables the use of existing Bioconductor packages for analysis, as its classes are extended from the ExpressionSet class. The package provides a workflow pipeline for Illumina data analysis, starting from raw data through functional analysis. The lumi package is an important tool for processing Illumina microarray data and has been improved through user contributions.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 features a variance-stabilizing transformation (VST) algorithm that utilizes technical replicates available on Illumina microarrays. It also provides multiple normalization methods and quality control plots. A vendor-independent nucleotide universal identifier (nuID) was developed to uniquely identify Illumina probes, enabling version- and vendor-independent annotation. The nuID allows for accurate encoding of probe sequences and error checking. The lumi package is built upon the ExpressionSet class in Bioconductor, enabling interoperability with other Bioconductor packages. It includes a LumiBatch class that holds data, control probe information, and quality control summaries. The package includes methods for preprocessing and quality control, such as lumiR, lumiB, lumiT, lumiN, and lumiQ, which together form a preprocessing pipeline. A lumiExpresso method encapsulates all four methods into one. The package also provides various plot functions for visualization and quality control. The annotation packages in lumi use nuID as the identifier for probes, allowing for version- and vendor-independent annotation. These packages can be downloaded from Bioconductor and are designed for different Illumina expression chips. The lumi package enables the use of existing Bioconductor packages for analysis, as its classes are extended from the ExpressionSet class. The package provides a workflow pipeline for Illumina data analysis, starting from raw data through functional analysis. The lumi package is an important tool for processing Illumina microarray data and has been improved through user contributions.