It is kind of shame as I did not save the “dat” object when I did the micorRNA array data analysis for Mahmet. Mahmet recently requested for the “expression” data for the microRNA affyarray data. I realized that my R code is NOT working anymore. Here are the error messages

dat <- read.celfiles (filenames=paste(celpath,pheno$ChipBarcode,".CEL",sep=""), sampleNames=rownames(pheno), phenoData=pheno)

##===================================================================================
#Error in checkSlotAssignment(object, name, value) :
# assignment of an object of class “data.frame” is not valid for slot ‘phenoData’ in an object of class “ExpressionFeatureSet”; is(value, “AnnotatedDataFrame”) is not TRUE
#Error during wrapup: cannot open the connection
##====================================================================================

With the following command:

# The following command works, but RMA will fail (also pvac) because this it
# NOT an AffyBatch
dat <- read.celfiles (filenames=paste(celpath,pheno$ChipBarcode,".CEL",sep=""))
pData(dat) <- pheno
dt.rma = rma(dat) # run RMA algorithm

#Error in (function (classes, fdef, mtable) :
# unable to find an inherited method for function ‘probeNames’ for signature ‘”ExpressionFeatureSet”’
#Error during wrapup: cannot open the connection

It definitely worked in the past. However, the consequences are that I have to redo it!

Let’s look at the cdf for microRNA array

Some debate on AffyBatch vs oligo pacakges