[BioC] Coercing matrix into expression set, for normalization of only subsets of miRNAs (affy miRNA3.0)

Dana Most danamost at gmail.com
Wed Oct 23 06:04:31 CEST 2013

Dear All,

How can I transform/coerce a gene expression matrix into an expression set?

I'm using affy miRNA 3.0 data and I would like to normalize only a subset of 
the samples (i have 4 groups of samples and would like to choose 2) and only a 
subset of microRNAs (I have mature and premature microRNAs and they should not 
be normalized together).

It should look something like this:
affyExpressionFS <- read.celfiles(celFiles, pkgname="pd.mirna.3.0")
data = exprs(affyExpressionFS)
data = data[1:1000,1:20]

exprsData = coerce data into expression set


Also, I would like to use array quality metrics package on exprsData

arrayQualityMetrics(expressionset = exprsData,
outdir = "exprsData",force = FALSE, do.logtransform = FALSE)

Thank you,

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