[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
rma(exprsData)
Also, I would like to use array quality metrics package on exprsData
arrayQualityMetrics(expressionset = exprsData,
outdir = "exprsData",force = FALSE, do.logtransform = FALSE)
Thank you,
Dana
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