Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments
We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data outputs and quality control assessments and explore the commands to perform such analysis.
Key wordsMicroarrays Genomic profiling Tumor Illumina Bead arrays R Normalization Quality control
GH is grateful for MUSC College of Medicine Institutional start-up funds. We thank Dr. Willian A da Silveira for critical reading of the manuscript.
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