[Bioc-devel] ExpressionSet for qRT-PCR

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


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