Hello,

I am analyzing microarray data and i am little bit new to R programming. it
has 4 different sample with 3 replicate each. I went upto background
correction but i found difficult in normalization and getting duplicate
correlation. can you help me in further process

Thank you in advance.

library(limma)

> getwd()

[1] "/Users/nirajnepal/Documents/codata"

> datadir <- system.file("codata")

> library(RColorBrewer)

> targets <- readTargets("targets.txt")

> cols <- brewer.pal(12, "Set3")

> RG <- read.maimages(targets$FileName, source="genepix",
columns=list(Rf="F635 Mean",Gf="F635 Mean",Rb="B635 Median",Gb="B635
Median"))

Read Cnt.1.gpr

Read Cnt.2.gpr

Read Cnt.3.gpr

Read Day1.1.gpr

Read Day1.2.gpr

Read Day1.5.gpr

Read Day3.1.gpr

Read Day3.2.gpr

Read Day3.3.gpr

Read Day90.2.gpr

Read Day90.3.gpr

Read Day90.4.gpr

> pData <- data.frame(population = c('a', 'a', 'a','b', 'b',
'b','c','c','c','d','d','d'))

> rownames(pData) <-  RG$targets$FileName

> design <- model.matrix(~factor(pData$population))

> gene <- grep("GE", RG$genes$ID)

> RG.final <- RG[gene, ]

> boxplot(data.frame(log2(RG.final$Rb)),main="Background", col=cols)

> boxplot(data.frame(log2(RG.final$R)),main="Foreground", col=cols)

> RGb <- backgroundCorrect(RG.final, method="subtract")

> boxplot(data.frame(log2(RGb$R)),main="Backgroud Correction", col=cols)

There were 13 warnings (use warnings() to see them)

> library(Biobase)

> library('vsn')

> y2 <- normalizeVSN(RGb$R)

vsn2: 35891 x 12 matrix (1 stratum). Please use 'meanSdPlot' to verify the
fit.

> boxplot(as.data.frame(log2(y2)), main="Normalized intensities", col=cols)

> corfit <- duplicateCorrelation(y2, design, ndups=3)

Loading required package: statmod

Error in dim(M) <- c(spacing, ndups, ngroups, nslides) :

  dims [product 430668] do not match the length of object [430692]
-- 
*Niraj Nepal*
*

Research Assistant
*
*Cell and Molecular Physiology Lab*
*West Virginia Sta**te University*
*Institute, WV*

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