Tutorial:From Data import to Normalization in Microarray Analysis using in R (Part I)
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8.0 years ago
majuang66 ▴ 140

I want to share my re-analysis and understanding of published microarray data of GEO database and others. I will update consistently the results...... and I can not write English well ^.^!!! Example 1: GSE4536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4536)

# Open R
# Install the bioconductor packages, if not already installed
source("http://bioconductor.org/biocLite.R")
# Affymetrix Chip
biocLite("affy")

library(affy)
# Data Download for CEL files - I use Filezillla

Connect ftp.ncbi.nlm.nih.gov

Download the GSE4536 and unzip the GSE4536 zip file using the 7-zip

# Import into R from your local storage
setwd("e:/GSE4536 microarray")

mydata_GSE4536<-ReadAffy()
# Normalize to raw data (mydata_GSE4536)
# RMA normalization
mydata_GSE4536_rma<-rma(mydata_GSE4536)
# MAS5 normalization
mydata_GSE4536_mas5<-mas5(mydata_GSE4536)
# GC-RMA normalization
biocLite("gcrma")

library(gcrma)

mydata_GSE4536_gcrma<-gcrma(mydata_GSE4536)
# Farms normalization
biocLite("farms")

library(farms)

mydata_GSE4536_farms<-qFarms(mydata_GSE4536)
# dchip normalization
mydata_GSE4536_dchip<-expresso(mydata_GSE4536,normalize.method="invariantset",bg.correct=FASE,pmcorrect.method="pmonly",summary.method="liwong")

Reference

  1. http://repository.countway.harvard.edu/xmlui/bitstream/handle/10473/4710/Bioconductor_Manual.doc?sequence=1
  2. Using FARMS for summarization Using I/NI-calls for gene filtering
gene R • 5.5k views
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Your English is very good - do not worry.

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Thank you for your reply. I have studied english everyday!

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