[BioC] rma for tiling arrays (oligo package)

[Ben Bolstad]

Actually, you can avoid "copying from affy" altogether by using
preprocessCore directly where both normalize.quantiles() and 
rma.background.correct() are actually defined. 

I think oligo also loads preprocessCore, so those functions should
already be exposed.

Ben





On Mon, 2008-07-21 at 10:48 -0400, James W. MacDonald wrote:
> 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
> 
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