Question: Computing NUSE and RLE scores
1
gravatar for beverly893
4.8 years ago by
beverly89310
United States
beverly89310 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.

affyplm rle nuse • 1.3k views
ADD COMMENTlink modified 4.8 years ago by Sean Davis21k • written 4.8 years ago by beverly89310
Answer: Computing NUSE and RLE scores
0
gravatar for Sean Davis
4.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

To answer your question, directly, you cannot use NUSE and RLE on an ExpressionSet.

I'd suggest reading the vignette from affyPLM on Quality Control for details. That said, the ReadAffy() function returns an AffyBatch that you can then use for the affyPLM NUSE and RLE functions.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Sean Davis21k
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