[BioC] affyPara - rmaPara fails using cdfname

Mon Jun 18 15:51:34 CEST 2012

Dear

I am investigating whether affyPara can be used to analyze a large number of Microarray data.
As a test case I have 20 CEL files. This works just fine running

	...	
	expressionSetRma<- rmaPara(files)
	...

If I want to use the "cdfname" parameter however

	...
	expressionSetRma<- rmaPara(files, cdfname="hgu133plus2hsentrezg", verbose=TRUE)
	...

I receive following error:

	Error in dimnames(eset_mat) <- list(ids, samples.names) :
	  length of 'dimnames' [1] not equal to array extent
	Calls: rmaPara -> preproPara -> .doSummarizationPara
	In addition: Warning messages:
	1: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4'
	2: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4'
	Execution halted

I saw a thread http://answerpot.com/showthread.php?1408276-affyPara mentioning a bug in the .initAffyBatchSF function date 21/10/2010.
Might this be the same bug ?

Many thanks for your help and/or ideas.

Kind Regards

Yves Wetzels
Contractor on behalf of
Janssen 
Turnhoutseweg 30
B-2340-Beerse, Belgium

Below you`ll find the logfile/environment settings for both test runs.

******************************************************************
Log for expressionSetRma<- rmaPara(files) => OK

******************************************************************
ubuntu at ip-10-239-95-215:~/test$ cat runAffyPara.R.log.withoutcdf

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(affyPara)
Loading required package: affy
Loading required package: BiocGenerics

Attaching package: âBiocGenericsâ

The following object(s) are masked from âpackage:statsâ:

    xtabs

The following object(s) are masked from âpackage:baseâ:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: snow
Loading required package: vsn
Loading required package: aplpack
Loading required package: tcltk
Loading Tcl/Tk interface ... done

Attaching package: âaffyParaâ

The following object(s) are masked from âpackage:snowâ:

    makeCluster, stopCluster

Warning message:
In fun(libname, pkgname) : no DISPLAY variable so Tk is not available
> library(hgu133plus2hsentrezgcdf)
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 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 affyPara_1.16.0
[3] aplpack_1.2.6                  vsn_3.24.0
[5] snow_0.3-9                     affy_1.34.0
[7] Biobase_2.16.0                 BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] affyio_1.24.0         BiocInstaller_1.4.6   grid_2.15.0
[4] lattice_0.20-6        limma_3.12.1          preprocessCore_1.18.0
[7] tools_2.15.0          zlibbioc_1.2.0
> path <- "/home/ubuntu/test/cel_files"
> makeCluster(2)
> files <- list.celfiles(path, full.names=TRUE)
> files
 [1] "/home/ubuntu/test/cel_files/GSM686287.CEL"
 [2] "/home/ubuntu/test/cel_files/GSM686289.CEL"
 [3] "/home/ubuntu/test/cel_files/GSM686290.CEL"
 [4] "/home/ubuntu/test/cel_files/GSM686291.CEL"
 [5] "/home/ubuntu/test/cel_files/GSM686298.CEL"
 [6] "/home/ubuntu/test/cel_files/GSM686300.CEL"
 [7] "/home/ubuntu/test/cel_files/GSM686301.CEL"
 [8] "/home/ubuntu/test/cel_files/GSM686303.CEL"
 [9] "/home/ubuntu/test/cel_files/GSM686304.CEL"
[10] "/home/ubuntu/test/cel_files/GSM686305.CEL"
[11] "/home/ubuntu/test/cel_files/GSM686310.CEL"
[12] "/home/ubuntu/test/cel_files/GSM686311.CEL"
[13] "/home/ubuntu/test/cel_files/GSM686314.CEL"
[14] "/home/ubuntu/test/cel_files/GSM686316.CEL"
[15] "/home/ubuntu/test/cel_files/GSM686319.CEL"
[16] "/home/ubuntu/test/cel_files/GSM686320.CEL"
[17] "/home/ubuntu/test/cel_files/GSM686322.CEL"
[18] "/home/ubuntu/test/cel_files/GSM686323.CEL"
[19] "/home/ubuntu/test/cel_files/GSM686324.CEL"
[20] "/home/ubuntu/test/cel_files/GSM686325.CEL"
> expressionSetRma<- rmaPara(files)
Loading required package: AnnotationDbi

Attaching package: âhgu133plus2cdfâ

The following object(s) are masked from âpackage:hgu133plus2hsentrezgcdfâ:

    i2xy, xy2i

Warning messages:
1: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(xel) : is.na() applied to non-(list or vector) of type 'S4'
> stopCluster()
> write.exprs(expressionSetRma,file="/home/ubuntu/test/expressionSetRma.Rda")
>

******************************************************************
Log for expressionSetRma<- rmaPara(files) => ERROR

******************************************************************
ubuntu at ip-10-239-95-215:~/test$ more runAffyPara.R.log.withcdf

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)