[BioC] affyPara: background correction & normalization only?

[Markus Schmidberger]

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.
Do not use the unstable 2.11 version. Please use version 2.10.
I will check for these warnings as soon there is a code freeze for 2.11.
I will add the none to the summary.method list. Thanks!

Best
Markus
>
>
> 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