normalization_via_cyclicLOESS.rtf

{\rtf1\ansi\ansicpg1252\cocoartf2580
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 Helvetica;}
{\colortbl;\red255\green255\blue255;}
{\*\expandedcolortbl;;}
\paperw11900\paperh16840\margl1440\margr1440\vieww10800\viewh8400\viewkind0
\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\pardirnatural\partightenfactor0

\f0\fs24 \cf0 ## Write normalization function (cyclic LOESS normalization on log2-transformed reporter ion intensities)\
library(limma)\
loess_norm <- function(m)\{\
  m[m==0] <- NA\
  m_log <- log2(m)  \
  m_norm <- 2^normalizeBetweenArrays(m_log, method="cyclicloess", cyclic.method = "fast")\
  return(m_norm)\
\}\
}