hi,
i have some CEL file and i did like below but i have X244901_at while i need AGI code even i used cdf
library(affy)
library(vsn)
library(limma)
library(altcdfenvs)
library(simpleaffy)
# listing the cel files
celFiles <- list.celfiles()
# assigning the cel files to affyraw variable
affyraw=ReadAffy(filenames = celFiles)
# making cdf file
tmp.env=make.cdf.env("ATH1121501_At_TAIRG.cdf")
# performing vsn normalization
vsn.data <- expresso(affyraw, normalize.method="vsn", bg.correct=F, pmcorrect.method="pmonly", summary.method="medianpolish")
# examining the normalization
boxplot(affyraw,col="red")
plot(exprs(affyraw)[,1:2], log = "xy", pch=".",
main="all")
# writing the result
write.table(vsn.data, file = "vsn1.txt", dec = ".", sep = "\t", quote = FALSE)
head(vsn.data[,1:2])
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1 features, 2 samples
element names: exprs, se.exprs
protocolData
sampleNames: Col-0 24h primed.CEL.CEL Col-0 24h unprimed.CEL.CEL
varLabels: ScanDate
varMetadata: labelDescription
phenoData
sampleNames: Col-0 24h primed.CEL.CEL Col-0 24h unprimed.CEL.CEL
varLabels: sample
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: ath1121501
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what is my fault please in the above code??? even i scared maybe i have written an incomplete normalized file
thank you,
my insisting on writing the data in a txt file is because i need the normalized file as an input for another tool for GRN inference anyway i did like below
i only need a vsn normalized file that the rownames are AGI code not _at
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