Hi,

I have already analyzed some gene expression data using RMAExpress, writing
to a tab-delimited file and then using the SAM plugin for MS Excel.  I had
great results and didn't have to use R at all.  Now I would like to repeat
the process using R.

I don't really understand how to work with eSets or ExpressionSets, which is
what the affy package stores expression data in; and I don't think the samr
package even uses these objects...

Anyways, here is the workflow I am trying to do in R:

* Read .CDF file for RAE230A,
* Read .CEL files for 12 RAE230A Genechips
* Compute RMA expression measures using background adjustment and quantile
normalization (default median polish for summarization)
* Log 2 transform the expression measures

....repeat for 12 RAE230B Genechips

* Join the data from RAE230A and RAE230B into one table; probesets with
identical names will have ##rae230a or ##rae230b appended to their name or
some other method can be used to differentiate probesets with identical
names between the two chips.

* Label the the samples according to three experimental groups, (i.e.
"1","2","3")

* Use SAM with samr to create a list of genes with pFDR ~ 5%

How much of a headache would it be to do this in R?  Is there a quick way to
convert an Expression Set to a format usable by samr?  Has anyone else used
the same combination (affy and samr)?

Thanks in advance.
-R

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