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Bert Gunter
Genentech Nonclinical Biostatistics
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"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll
On Fri, Feb 6, 2015 at 9:27 PM, Beverly Nguyen <beverly893 at gmail.com>
wrote:> 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.
> ?
>
> [[alternative HTML version deleted]]
>
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