[BioC] Coercing Normalized Data to exprSet

Barry Henderson barry.henderson@ribonomics.com
Tue, 4 Feb 2003 09:47:07 -0500

Dear List
I have a set of two color array data I am trying to analyze with
BioConductor.  The experiment is of a loop design.  I have read the data
in and conormalized it leaving me with a marrayNorm object.  I have
coerced that object into an exprSet object and I am now trying to
understand how to filter/test on that object.  Since the individual
channels of the two color array data have been collapsed into a single
log ratio in the exprSet object, assigning covariates to individual
channels (samples) seems unobvious.  
Am I missing something?  Is this a challenge in dealing with loop
designs?  Or is this a limitation of BioConductor with respect to this
experimental design?  
Can I calculate the normalized expression, write the values out and then
read them back in as an exprSet?  If so, is there a facile way to handle
this process.  I've been through the docs, vignettes, and worked with
the eset provided with BioBase but it simply isn't obvious to me how to
work with two color, loop designs.
Thanks in advance for any advice.  I have pasted excerpts of the
marrayNorm (normalized.data) and exprSet (tox2) objects I am working
with below.  As you can see 45 arrays get collapsed into 45 samples...
As an added note, I have calculated normalized intensity values and
written them out for input into maanova but I would like to undertand
how to do this in BioConductor if possible.
Barry Henderson
> normalized.data
Normalized intensity data:       Object of class marrayNorm.
Number of arrays:       45 arrays.
A) Layout of spots on the array: 
Array layout:    Object of class marrayLayout. 
Total number of spots:                  2688
Dimensions of grid matrix:              4 rows by 4 cols
Dimensions of spot matrices:            12 rows by 14 cols
Currently working with a subset of 2688 spots.
Control spots: 
There are   2 types of controls : 
Control  normal 
    208    2480 

Notes on layout: 
B) Samples hybridized to the array: 
Object of class marrayInfo. 
    maLabels # of slide            Names Experiment Cy3 Experiment Cy5
1   34-108-1   34-108-1  34-108-1.Rinput          Wyeth    Bezafibrate
2   34-108-2   34-108-2  34-108-2.Rinput     Lovastatin          Wyeth
3   ...
> tox2
Expression Set (exprSet) with 
        2688 genes
        45 samples
                 phenoData object with 6 variables and 45 cases
                : # of slide
                : Names
                : Experiment Cy3
                : Experiment Cy5
                : date
                : Comments

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