[BioC] affyPara: background correction & normalization only?
Markus Schmidberger
schmidb at ibe.med.uni-muenchen.de
Mon Mar 8 10:54:29 CET 2010
fixed everything in 1.7.2.
Thanks for using affyPara and providing feedback.
Best
Markus
Leo Lahti wrote:
> Dear Markus,
>
> Thanks for a quick reply.
>
>
> I tested affyPara 1.7.1. To get the summarization method 'none' to
> work, I had to slightly modify the summary.method check in preproPara
> R code ("if ((any( express.summary.stat.methods()==summary.method) ||
> summary.method == "none") == 0) stop("Unknown
> Summarization-Method")"). After this the summary.method "none" seems
> to be functional in preproPara function.
>
>
> However, I bumped into another problem which seems to be related to
> the affyPara warnings in build/check at
> http://bioconductor.org/checkResults/2.6/bioc-LATEST/
> I could not so far solve this issue so far. Any
> solutions/updates/feedback would be appreciated.
>
>
> You can find the output of my running example below.
>
>
> with kind regards
> Leo Lahti
> leo.lahti at iki.fi <mailto:leo.lahti at iki.fi>
> http://www.cis.hut.fi/lmlahti
>
>
> > require(affyPara)
> > require(hgu133plus2cdf)
> Loading required package: hgu133plus2cdf
> > require(hgu133plus2hsentrezgcdf)
> Loading required package: hgu133plus2hsentrezgcdf
> > cl <- makeCluster(3, type = "SOCK")
> > cels <- list.celfiles("/my/CEL/path", full.names = TRUE)
> >
> > eset <- preproPara(cels,
> + bgcorrect = TRUE, bgcorrect.method = "rma",
> + normalize = TRUE, normalize.method = "quantiles",
> + pmcorrect.method = "pmonly",
> + summary.method = "none",
> + cdfname = "HGU133Plus2_Hs_ENTREZG", cluster = cl, verbose
> = TRUE)
> Partition of object Error in gsub("^/?([^/]*/)*", "", unlist(object),
> extended = TRUE) :
> unused argument(s) (extended = TRUE)
> > sessionInfo()
> R version 2.11.0 Under development (unstable) (2010-02-15 r51142)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tcltk stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] hgu133plus2hsentrezgcdf_12.1.0 hgu133plus2cdf_2.5.0
> [3] affyPara_1.7.1 aplpack_1.2.2
> [5] vsn_3.15.1 snow_0.3-3
> [7] affy_1.25.2 Biobase_2.7.4
>
> loaded via a namespace (and not attached):
> [1] affyio_1.15.2 grid_2.11.0 lattice_0.18-3
> [4] limma_3.3.9 preprocessCore_1.9.0 tools_2.11.0
>
> On Fri, Mar 5, 2010 at 2:02 PM, Markus Schmidberger
> <schmidb at ibe.med.uni-muenchen.de
> <mailto:schmidb at ibe.med.uni-muenchen.de>> wrote:
>
> Dear Leo,
>
> good point.
>
> I did some changes to preproPara(). No there is a summarization
> method 'none' (summary.method='none') available. There will be no
> summarization step and the results object eset is NULL.
> I submitted these changes and documentation to the svn. Version
> 1.7.1. should be available ad midnight:
> http://www.bioconductor.org/packages/devel/bioc/html/affyPara.html
>
> Now at all nodes the bgc and normalized affyBatches are available
> in the GlobalEnvironment. It is very simple to run some code on that.
>
> res <- clusterCall(cluster, FUN)
> FUN<- function()
> {
> require(affy)
> if (exists("AffyBatch", envir = .GlobalEnv))
> AffyBatch <- get("AffyBatch", envir = .GlobalEnv)
>
> # do anything you want on the AffyBatch.
> }
>
> res will be a list of results from all nodes. You have to find a
> way to combine these results.
>
> Best
> Markus
>
>
>
>
> Leo Lahti wrote:
>
> Dear affyPara package maintainers and BioC developer community,
>
>
> The parallelizations of Affy preprocessing in the affyPara
> package provide essential tools to handle large array collections.
>
> Before starting to hack on this myself, I would like to ask if
> there are workarounds in affyPara to obtain a preprocessed &
> normalized (but not summarized) PM intensity matrix from CEL
> files? Alternatively, having an access to virtual affybatch
> (i.e. keeping it in the nodes without 'rebuild') would solve
> the problem. Is such functionality available?
>
> I would need the probe-level values (for PM probes) after
> preprocessing and normalization (but without probeset
> summarization step) - in an ideal case a probes x arrays
> matrix, and not necessarily other information from the
> affybatch object. It seems that both background correction and
> normalization can be done in affyPara by reading in the CEL
> files directly. However, the output of these methods in itself
> an affybatch which will cause the memory problems the package
> is trying to solve.
>
> Thanks once more for relevant work.
>
> with kind regards
>
> Leo Lahti
> Department of Information and Computer Science
> Aalto University School of Science and Technology
> Finland
>
>
>
> --
> Dr. rer. nat. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Lehrstuhl für Biometrie und Bioinformatik
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger
> [at] ibe.med.uni-muenchen.de <http://ibe.med.uni-muenchen.de>
>
>
--
Dr. rer. nat. Markus Schmidberger
Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Lehrstuhl für Biometrie und Bioinformatik
Marchioninistr. 15, D-81377 Muenchen
URL: http://www.ibe.med.uni-muenchen.de
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
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