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@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@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
>
>

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