Hi everyone,



I am new in using Oligo-Bioconductor.  I do have some basic questions as
how to analyze my hg 1.1 st array.  I used following command lines:



source("http://bioconductor.org/biocLite.R")

    biocLite("pd.hugene.1.1.st.v1")

source("http://bioconductor.org/biocLite.R")

    biocLite("oligo")



library(oligo)

celFiles <- list.celfiles()

Data <- read.celfiles(celFiles)

ppData <- rma(Data)

boxplot(ppData)

expData <- exprs(ppData);

boxplot(expData)

write.csv(expData, file = "MyData.csv");


When I looked at the boxplots annotating ppData, and expData, I noticed
that ppData was nicely normalized and showed a completely normal
distribution whereas expData had huge outliers.


I)       Which one is the output data?  ppData, or expData?

II)    Should I apply limma on expData or ppData?

III)  How could I prepare the data for limma?  May I use a .csv file to
satrt limma analysis?



Thanks,
Jerry

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