[R] Computing RLE and NUSE Scores

[Bert Gunter]

Ask on the BioConductor list, not here.



Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"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.
> ᐧ
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.