[Bioc-devel] ExpressionSet for qRT-PCR

Mon Jan 15 19:12:55 CET 2007

Hello Martin,

thanks for your hints!
I will take them up for my package.

Best regards,
Matthias

Martin Morgan schrieb:
> "Matthias Kohl" <Matthias.Kohl at stamats.de> writes:
>
>   
>> 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
>>     
>
> If the data is really quite different from that currently stored in
> ExpressionSet (i.e., gene expression data from microarray experiments)
> then probably you want to create a new class for the data. This will
> help associate appropriate methods with appropriate data.
>
> This does NOT mean starting a new class, say qtPCRSet, from
> scratch. If qtPCRSet is a specialized version of ExpressionSet data
> (you'd like functionality that is unique to qtPCR, in addition to the
> analytic methods available to ExpressionSet) then you would subclass
> ExpressionSet.
>
> It seems that a more likely starting point is that you want to have
> the overall coordination of assay data + phenotypic data + feature
> data + experiment data + annotation, but the data analysis methods
> relevant to qtPCRSet are different from those for ExpressionSet. Then
> the starting point is eSet
>
>   
>> setClass("qtPCRSet", contains="eSet")
>>     
> [1] "qtPCRSet"
>   
>> new("qtPCRSet")
>>     
> qtPCRSet (storageMode: lockedEnvironment)
>   element names:  
> phenoData
>   sampleNames: none
>   varLabels and varMetadata: none
> featureData
>   featureNames: none
>   varLabels and varMetadata: none
> experimentData: use 'experimentData(object)'
> Annotation character(0)
>
> and you'll have lots of functionality (e.g., coordinated subsetting,
> display, access to slots via phenoData(), etc) already available (the
> 'initialize' method might be tricky to get exactly right, but
> ExpressionSet provides a model). More info is in the vignette "Notes
> for eSet developers".
>
> Martin
>
>   
>> - 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 ----
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>     
>
>   

-- 
Dr. rer. nat. Matthias Kohl
E-Mail: matthias.kohl at stamats.de
Home: www.stamats.de