[Bioc-devel] ExpressionSet for qRT-PCR

[James W. MacDonald]

Hi Martin,

Thanks! As usual, a perfectly lucid explanation and example.

Best,

Jim

Martin Morgan wrote:
> Hi Jim --
> 
> Saving the additional information in featureData (at least, the
> information that is unique to the ExpressionSet) sounds like the right
> idea.
> 
> The 'data' slot of AnnotatedDataFrame *is* meant for data like this --
> think of each column as a column in a standard data.frame. The
> varMetadata slot is meant to be a description of the column itself --
> maybe a 'data' column would be called 'well', and since this is quite
> ambiguous the varMetadata column 'labelDescription' might be "Maps row
> to SuperArray well" (each column in 'data' must have a corresponding
> 'labelDescription').
> 
> The "AnnotatedDataFrame" part of the ExpressionSet might be
> constructed like
> 
> new("AnnotatedDataFrame",
>     data=data.frame(
>       well=1:96),
>     varMetadata=data.frame(
>       labelDescription="Maps row to SuperArray well"))
> 
> You might incorporate this into 
> 
> eg <- new("ExpressionSet",
>           exprs=matrix(rnorm(96*20), 96),
>           featureData=new("AnnotatedDataFrame",
>             data=data.frame(
>               well=1:96),
>             varMetadata=data.frame(
>               labelDescription="Maps row to SuperArray well"))
>           )
> 
> There can be more than 'well' in 'data', and addition varMetadata
> (e.g., for phenoData, varMetadata might contain information about
> the scale on which the phenotypic variable was measured). These can be
> added, to; one way is
> 
> featureData(eg)$another <- letters[1+1:96 %% 8]
> varMetadata(featureData(eg))["another", "labelDescription"] <-
>   "Some additional info"
> head(pData(featureData(eg)))
> 
> and used:
> 
> which(featureData(eg[10:1,])$well == 2)
> 
> Martin
> 
> "James MacDonald" <jmacdon at med.umich.edu> writes:
> 
> 
>>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, 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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Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.