[Bioc-devel] ExpressionSet for qRT-PCR

James W. MacDonald jmacdon at med.umich.edu
Sat Jan 13 15:56:48 CET 2007

Hi Matthias,

Matthias Kohl wrote:
> 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
> http://bioconductor.org/uploadPackage/
> about two weeks ago, but did not get any feed-back so far.

I have been looking at your package a bit, but have not had the time yet 
to give a reasonable review.

> Which methods do you want to add to your package?

Probably nothing fancy. I like the idea of having some quantitative way 
to decide which control gene to use for normalization (as implemented in 
your SLqPCR package), but for differential expression I was only 
thinking about delta-deltaCT when there is no replication, and simple 
t-tests (or possibly using limma's empirical Bayesian variance adjusted 
t-tests) when there is replication.

I'm not yet sure I want to create an actual package for release. My core 
has started offering SuperArrays to our clients, and if I am going to be 
seeing a lot of them, I wanted to have a consistent framework in place 
for the analyses.

What sort of analyses were you planning on adding to SLqPCR? Are you 
intending this package for the analysis of arbitrary PCR data, or a 
particular platform?



> Best regards
> Matthias
> 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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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

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