Thanks Ben, I forgot that you moved everything into preprocessCore. Best, Jim Ben Bolstad wrote: > 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.ti grv5") >>>> 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Hildebrandt Lab >> 8220D MSRB III >> 1150 W. Medical Center Drive >> Ann Arbor MI 48109-0646 >> 734-936-8662 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662