ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).
|Author||Yuliya V Karpievitch, Tim Stuart and Sufyaan Mohamed|
|Bioconductor views||DifferentialExpression ImmunoOncology MassSpectrometry Normalization Proteomics|
|Maintainer||Yuliya V Karpievitch <[email protected]>|
|Package repository||View on Bioconductor|
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