[BioC] rma for tiling arrays (oligo package)

[James W. MacDonald]

Hi Ann,

I don't think you want to use rma() directly, as it is going to try to 
do a medianpolish on probesets but such a thing doesn't exist for the 
tiling arrays.

If you want to use the background correction and normalization that are 
used by rma() then I think it will take some work on your part. The 
functions you will want to use are part of the affy package, but you 
don't really want to load affy and oligo at the same time because there 
are so many identically named functions (they both have namespaces, so 
this isn't the end of the world, but it is easier if you don't have to 
deal with name collisions).

I would personally just copy the functions normalize.quantiles() and 
rma.background.correct() from affy into a file (say, affysources.R) and 
then source that into R. Both of these functions want you to pass a 
matrix, so you would want to extract the pm data from your AllArrays 
object, run rma.background.correct() and then normalize.quantiles() on 
the matrix, and then put that back into AllArrays.

Best,

Jim



Ann Hess wrote:
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662