Bioconductor /R package panp: Presence-Absence Calls from Negative Strand Matching Probesets. A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. Paper: PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays

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  1. João Duarte; Vinícius Mayrink: slfm: An R Package to Evaluate Coherent Patterns in Microarray Data via Factor Analysis (2019) not zbMATH
  2. Mayrink, Vinicius D.; Lucas, Joseph E.: Bayesian factor models for the detection of coherent patterns in gene expression data (2015)
  3. Reme, Thierry; Hose, Dirk; De Vos, John; Vassal, Aurelien; Poulain, Pierre-Olivier; Pantesco, Veronique; Goldschmidt, Hartmut; Klein, Bernard: A new method for class prediction based on signed-rank algorithms applied to (Affymetrix(R)) microarray experiments (2008) ioport