It would be helpful to get some clarification on some, supposedly, simple
array facts;

Part1)

For 2 colour arrays, Mvalues!

Am I correct in thinking that M values from a two colour array are the same
as log2 fold change?
Cy5 = case, Cy3 = control and M = log2( case/control), so a log fold change
of -1 is 2 fold down-regulated etc?

For a 1 colour array, Mvalues will arise from array1 = case and arrray 2 =
control
So log2(array1/array2) is again the equivalent of log2 fold change.

with both these scenarios, I am right in stating that the raw fluorescent
signals are themselves log2 transformed to make plot distributions close to
normal?

Part2)

I use the marray package to extract array data, normalise and an impute
package to replace missing values for M values.
I make myself an expression set object using "new"

I then want to generate a dist object

> dd = dist(exprs(exampleSet))
Error in vector("double", length) :
  cannot allocate vector of length 582309001

or

> dd = dist(exampleSet)
Error in vector("double", length) :
  cannot allocate vector of length 582309001

It is probable I need to reduce the data set first as most genes are not
differentially expressed (as is the assumption with microarrays).
It would be great to understand these types of things more.

Thank you.

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