[BioC] rma for tiling arrays (oligo package)

[Ann Hess]

After creating an appropriate library using the makePDpackage, I am using 
the oligo package to open and work with Affymetrix Arabidopsis Tiling 1.0R 
Arrays.  I am interested in using the rma function to background correct 
and normalize the data, but I am not sure how to map the processed data 
back to probes or directly to chromosome and position.

What do the rownames of the expression matrix created by rma correspond 
to?  My best guess is that they correspond to chromosome position (which 
can be found using pmChr, but not for an ExpressionSet object).  However, 
these positions are relative to a particular chromosome and therefore not 
unique.  For example, there are probes corresponding to position 417 on 
both Chromosome 3 and Chromosome 5, but only a single row in the 
ExpressionSet object corresponding to 417.

Is there a way to background correct and normalize the data without the 
rma function?  Perhaps this would allow for easier mapping to probes.

Any suggestions would be appreciated.

Ann

Code and session info is here:

> library(oligo)
> library(pd.at35b.mr.v04.2.tigrv5)
> AllArrays<-read.celfiles(list.celfiles(),pk="pd.at35b.mr.v04.2.tigrv5")
> dim(pm(AllArrays))
[1] 3092374      12
> dim(mm(AllArrays))
[1] 3092338      12

> Pos<-pmPosition(AllArrays)
> length(Pos)
[1] 3092374
> length(unique(Pos))
[1] 2921991

> RMAout<-rma(AllArrays)

> dim(exprs(RMAout))
[1] 2921991      12

> exprs(RMAout)[1:10,1:2]
          Comp5-1_1006.CEL Comp5-2_1006.CEL
0                3.344400         3.295634
1                1.988137         1.708682
1000             6.315857         7.297425
10000009         9.053133         8.754469
10000014         2.106050         2.137780
10000024        10.392988         9.385502
10000026         2.242264         5.487639
10000034         1.830658         5.239400
1000004          3.097441         5.825040
10000046         6.839724         7.221181

> sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-redhat-linux-gnu

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] pd.at35b.mr.v04.2.tigrv5_1.2.0 oligo_1.2.2
[3] oligoClasses_1.0.3             affxparser_1.10.2
[5] AnnotationDbi_1.0.6            preprocessCore_1.0.0
[7] RSQLite_0.6-9                  DBI_0.2-4
[9] Biobase_1.16.3

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17