R/normalization.r

In RaikOtto/GeneraPipe:

normalize = function(results, chip_type, zipped, normalize){
  
  raw_data = results@raw_data
  cohorts_vec = results@cohorts_vec
  
  if (chip_type %in% c("hgu133a", "hgu133plus2", "drosophila2")){
    eset = affyPLM::threestep(raw_data, background.method = normalize[1], normalize.method = normalize[2], summary.method = normalize[3])

  } else if (chip_type %in% c("pd.huex.1.0.st.v2")){
    eset = oligo::rma(raw_data, target = 'extended', normalize = TRUE)
    Biobase::featureData(eset) = oligo::getNetAffx(eset, 'transcript')

  } else if ( chip_type %in% c("pd.hugene.2.0.st") ){
    eset = oligo::rma(raw_data, target = "core", normalize = TRUE)
    Biobase::featureData(eset) = oligo::getNetAffx(eset, 'transcript')

  } else {
    message(c("Unknown Chip Type: ", chip_type))
    stop()
  }
  
  # unify the names
  rownames(pData(eset)) = base::gsub(c(".gz|.CEL|.cel|.GZ"), "", rownames(pData(eset))) 
  mapping_cohort_p = match( base::gsub( c(".gz|.CEL|.cel|.GZ"), "", rownames(pData(eset))), base::gsub( c(".gz|.CEL|.cel|.GZ"), "", names(cohorts_vec)), nomatch = 0 )
  mapping_cohort_c = match( base::gsub( c(".gz|.CEL|.cel|.GZ"), "", names(cohorts_vec) ) , base::gsub( c(".gz|.CEL|.cel|.GZ"), "", rownames( pData(eset)) ) , nomatch = 0 )

  eset = eset[, rownames(pData(eset)) %in% base::gsub( c(".gz|.CEL|.cel|.GZ"), "", names(cohorts_vec))]
  pData(eset)$Cohort = cohorts_vec[mapping_cohort_p]
  
  results@eset = eset
  results
}