vsn and oligo (or xps?) packages for GeneST expression arrays
2
0
Entering edit mode
Tim Rayner ▴ 270
@tim-rayner-2913
Last seen 6.9 years ago
Hi, I'm curious to know whether there are any plans to support the use of the VSN algorithm (i.e. the vsn package) with the classes defined by the oligo package. The reason I ask is that it seems as though the latter package is now touted as one of the supported methods of handling Affymetrix GeneST expression arrays (e.g. HuGene, MoGene), but as far as I can see the only expression normalisation/summarisation method currently supported for objects of the oligo GeneFeatureSet class seems to be RMA. I'm not even sure if GCRMA is supported for GeneFeatureSet objects? I guess the same questions also apply to the xps package, although I suspect that VSN support would turn out to be more work to implement there given the rather different underlying object structures used by xps. Do please correct me if I'm wrong about any of this, but until now I've been forced to shoehorn our data into the old AffyBatch workflow using custom CDFs and I'd like to know if there's a better (i.e. supported) workflow I could be using. Best regards, Tim Rayner # Current setup for reference: > sessionInfo() R version 2.10.0 Patched (2009-11-03 r50305) x86_64-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] oligo_1.10.0 preprocessCore_1.8.0 oligoClasses_1.8.0 [4] gcrma_2.18.0 vsn_3.14.0 affy_1.24.2 [7] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.8 DBI_0.2-4 [5] grid_2.10.0 IRanges_1.4.9 lattice_0.17-26 limma_3.2.1 [9] splines_2.10.0 -- Bioinformatician Smith Lab, CIMR University of Cambridge
vsn oligo xps vsn oligo xps • 869 views
ADD COMMENT
0
Entering edit mode
@benilton-carvalho-1375
Last seen 16 months ago
Brazil/Campinas/UNICAMP
Hi Tim, yes, vsn support is planned. The affy and oligo packages share methods with the same name which come to be a problem when adding support for vsn. We already have agreed on a solution and it's just a matter of implementing these changes, which will greatly simplify this task. As soon as something is available (on the devel branch), I'll get back to the list. Cheers, b On Jan 4, 2010, at 2:06 PM, Tim Rayner wrote: > Hi, > > I'm curious to know whether there are any plans to support the use of > the VSN algorithm (i.e. the vsn package) with the classes defined by > the oligo package. The reason I ask is that it seems as though the > latter package is now touted as one of the supported methods of > handling Affymetrix GeneST expression arrays (e.g. HuGene, MoGene), > but as far as I can see the only expression > normalisation/summarisation method currently supported for objects of > the oligo GeneFeatureSet class seems to be RMA. I'm not even sure if > GCRMA is supported for GeneFeatureSet objects? I guess the same > questions also apply to the xps package, although I suspect that VSN > support would turn out to be more work to implement there given the > rather different underlying object structures used by xps. Do please > correct me if I'm wrong about any of this, but until now I've been > forced to shoehorn our data into the old AffyBatch workflow using > custom CDFs and I'd like to know if there's a better (i.e. supported) > workflow I could be using. > > Best regards, > > Tim Rayner > > > > # Current setup for reference: >> sessionInfo() > R version 2.10.0 Patched (2009-11-03 r50305) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] oligo_1.10.0 preprocessCore_1.8.0 oligoClasses_1.8.0 > [4] gcrma_2.18.0 vsn_3.14.0 affy_1.24.2 > [7] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.8 DBI_0.2-4 > [5] grid_2.10.0 IRanges_1.4.9 lattice_0.17-26 limma_3.2.1 > [9] splines_2.10.0 > > > > -- > Bioinformatician > Smith Lab, CIMR > University of Cambridge > > _______________________________________________ > 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
ADD COMMENT
0
Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 2.8 years ago
Austria
Dear Tim, Currently xps does not directly support vsn, however it is possible to combine xps with vsn, as the following code for the Affymetrix HuGene dataset demonstrates: 1, create ROOT scheme file and import HuGene CEL-files: ### new R session: load library xps > library(xps) # directory containing Affymetrix library files > libdir <- "/Volumes/GigaDrive/Affy/libraryfiles" # directory containing Affymetrix annotation files > anndir <- "/Volumes/GigaDrive/Affy/Annotation" # directory to store ROOT scheme files > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" # create ROOT scheme file for whole genome array HuGene > scheme.genome <- import.exon.scheme("Scheme_HuGene10stv1r4_na29_hg18",filedir=scmdir, paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene- 1_0-st-v1.r4.clf",sep="/"), paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene- 1_0-st-v1.r4.pgf",sep="/"), paste(anndir,"Version09Jul/HuGene- 1_0-st-v1.na29.hg18.probeset.csv",sep="/"), paste(anndir,"Version09Jul/HuGene- 1_0-st-v1.na29.hg18.transcript.csv",sep="/")) # directory containing Tissues CEL files > celdir <- "/Volumes/GigaDrive/ChipData/Exon/HuGene" # directory to store ROOT raw data files > datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData" # import tissues from Affymetrix Exon Array Dataset for HuGene- 1_0-st-v1 > celfiles <- c("TisMap_Breast_01_v1_WTGene1.CEL", "TisMap_Breast_02_v1_WTGene1.CEL", "TisMap_Breast_03_v1_WTGene1.CEL", "TisMap_Prostate_01_v1_WTGene1.CEL", "TisMap_Prostate_02_v1_WTGene1.CEL", "TisMap_Prostate_03_v1_WTGene1.CEL") # rename CEL files > celnames <- c("Breast01", "Breast02", "Breast03", "Prostate01", "Prostate02", "Prostate03") # import CEL files > data.genome <- import.data(scheme.genome, "HuTissuesGenome6", filedir=datdir, celdir=celdir, celfiles=celfiles, celnames=celnames) Note: It is suggested to rename the CEL-files and/or save copies of the original CEL-files, since importing the results from "vsn" requires conversion to CEL-files which may overwrite the original CEL-files! 2, convert raw data to expression levels using vsn and xps: ### new R session: # need to load xps after vsn (to be able to use intensity<-) > library(vsn) > library(xps) ### first, load ROOT scheme file and ROOT data file > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" > scheme.genome <- root.scheme(paste(scmdir,"Scheme_HuGene10stv1r4_na29_hg18.root",sep="/ ")) > datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData" > data.genome <- root.data(scheme.genome, paste(datdir,"HuTissuesGenome6_cel.root",sep="/")) # attach intensity to data > data.tmp <- attachInten(data.genome) > str(data.tmp) # get intensities as data.frame (includes X,Y) > tmp <- intensity(data.tmp) > head(tmp) # apply vsn2 to intensities only (w/o X,Y) > data.vsn2 <- vsn2(as.matrix(tmp[,3:ncol(tmp)])) # convert result from log2 > value <- as.data.frame(2^data.vsn2 at hx) # attach (X,Y) coordinates > value <- cbind(tmp[,1:2], value) > head(value) # replace data with value and save in ROOT file: # note: this step creates modified CEL-files! > intensity(data.tmp, "tmp_DataVSN", TRUE) <- value > str(data.tmp) # apply rma > datdir <- getwd() > data.norm <- rma(data.tmp, "tmp_data_norm", filedir=datdir, tmpdir="", background="none", normalize=FALSE, exonlevel="core+affx") > str(data.norm) > boxplot(data.norm) # get data.frame > expr.norm <- validData(data.norm) > head(expr.norm) I hope this example shows you how to use xps with vsn. In the long term I would like to implement vsn in xps, however this requires converting the relevant code to C++ and it is not easy to find out which parts of package vsn I need to convert. Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ Tim Rayner wrote: > Hi, > > I'm curious to know whether there are any plans to support the use of > the VSN algorithm (i.e. the vsn package) with the classes defined by > the oligo package. The reason I ask is that it seems as though the > latter package is now touted as one of the supported methods of > handling Affymetrix GeneST expression arrays (e.g. HuGene, MoGene), > but as far as I can see the only expression > normalisation/summarisation method currently supported for objects of > the oligo GeneFeatureSet class seems to be RMA. I'm not even sure if > GCRMA is supported for GeneFeatureSet objects? I guess the same > questions also apply to the xps package, although I suspect that VSN > support would turn out to be more work to implement there given the > rather different underlying object structures used by xps. Do please > correct me if I'm wrong about any of this, but until now I've been > forced to shoehorn our data into the old AffyBatch workflow using > custom CDFs and I'd like to know if there's a better (i.e. supported) > workflow I could be using. > > Best regards, > > Tim Rayner > > > > # Current setup for reference: > >> sessionInfo() >> > R version 2.10.0 Patched (2009-11-03 r50305) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] oligo_1.10.0 preprocessCore_1.8.0 oligoClasses_1.8.0 > [4] gcrma_2.18.0 vsn_3.14.0 affy_1.24.2 > [7] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.18.0 affyio_1.14.0 Biostrings_2.14.8 DBI_0.2-4 > [5] grid_2.10.0 IRanges_1.4.9 lattice_0.17-26 limma_3.2.1 > [9] splines_2.10.0 > > > >
ADD COMMENT

Login before adding your answer.

Traffic: 351 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6