[Bioc-devel] ExpressionSet for qRT-PCR

Matthias Kohl Matthias.Kohl at stamats.de
Sat Jan 13 09:20:47 CET 2007

Hi Jim,

I'm very interested in your work on qRT-PCR data.
I also work on a package to analyze qRT-PCR data. The first version of 
this package includes the methods described in Vandesompele et al (2002) 
(cf. http://www.gene-quantification.com/vandesompeles-2002.pdf). I want 
to add further methods for analyzing qRT-PCR data in near future and are 
also thinking about using an S4 class (if it works "ExpressionSet" or a 
derived class) to keep all data.

I submitted the first version of this package (SLqPCR) to


about two weeks ago, but did not get any feed-back so far.

Which methods do you want to add to your package?

Best regards

James MacDonald schrieb:
> 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?
> Best,
> Jim
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
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Dr. rer. nat. Matthias Kohl
E-Mail: matthias.kohl at stamats.de
Home: www.stamats.de

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