[Bioc-devel] ExpressionSet for qRT-PCR

James MacDonald jmacdon at med.umich.edu
Sat Jan 13 00:53:50 CET 2007

I'm thinking about writing some functions to analyze qRT-PCR data,
specifically the SuperArrays, which come in 96 or 384 well plates. I am
thinking that an ExpressionSet would be a nice container for these data,
and I hoped to get some advice.

The data I would want to put in the ExpressionSet would consist of the
cycle threshold values (numeric), which of course would go in the exprs
slot. SuperArray also supply a file that is essentially a 96 row matrix
that has the well, the gene symbol, the UniGene ID, Entrez Gene ID, and
the gene name. Ideally I would also like to stick these data in the
ExpressionSet as well, but I am not sure where. These data are part
annotation, and part location information. Since they map the genes to
the wells, I would like to keep them in the ExpressionSet (while
annotation data are supposed to be in an external package).

Is the featureData slot a good place? I can get it to go into the data
slot of an AnnotatedDataFrame, but not the varMetaData slot (which seems
like a more logical place).

Any suggestions?



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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