I am working on a project, and have been given a list of instructions as to
how to analyze microarray data. I am to use the affy and affyPLM packages
from Bioconductor.
I used ReadAffy() to read in my CEL files, then called rma() to normalize
the data. I now that this function returns an ExpressionSet.
I was then told to use the affyPLM package to compute the RLE and NUSE
scores in order to compute the median RLE and NUSE scores for each sample.
However, I am unable to call any of the package's function (fitPLM(),
NUSE(), RLE()) on the normalized data because it is an ExpressionSet.
My question is, how could I utilize the affyPLM package to compute RLE/NUSE
scores on an ExpressionSet, when the functions require the use of an
AffyBatch.
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