[Bioc-devel] ExpressionSet for qRT-PCR

[Matthias Kohl]

Hi Jim,

we work with 96 well plates (on the iQ5 platform of Bio-Rad).

The next steps I'm going to take in the near future are:
- add a function to read in the data for our platform
- use S4 class (ExpressionSet?) to save/hold the data
- implement further normalization strategies (with methods for "ExpressionSet", "matrix", "data.frame"?)
- add plot methods

So, the next versions of my package will mainly contain normalization strategies. 

Best regards,
Matthias


----- original message --------

Subject: Re: [Bioc-devel] ExpressionSet for qRT-PCR
Sent: Sat, 13 Jan 2007
From: James W. MacDonald<jmacdon at med.umich.edu>

> 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,
> 
> Jim
> 
> 
> > 
> > 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
> >>
> >>
> >> **********************************************************
> >> Electronic Mail is not secure, may not be read every day, and should 
> >> not be used for urgent or sensitive issues.
> >>
> >> _______________________________________________
> >> Bioc-devel at stat.math.ethz.ch mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>   
> > 
> > 
> > 
> 
> 
> -- 
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
> 
> 
> 
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues.
> 

--- original message end ----