[BioC] gcrma failed on mouse Gene 1.0 ST array

[Hooiveld, Guido]

Hi Yupu,

First: update to the latest version of R/BioC; the one you are using is quite old.

You may want to have a look at the suggestion Mike Smith proposed few months ago:
http://article.gmane.org/gmane.science.biology.informatics.conductor/32506

Note: I didn't try it myself, so I cannot comment any further on it.

HTH,
Guido

--------------------------------------------------------- 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:      guido.hooiveld at wur.nl
internet:   http://nutrigene.4t.com 
http://www.researcherid.com/rid/F-4912-2010


-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Yupu Liang
Sent: Thursday, September 29, 2011 17:59
To: bioconductor at r-project.org
Subject: [BioC] gcrma failed on mouse Gene 1.0 ST array

Hi,

I am trying to feed the mouse Gene 1.0 ST array into our R pipeline (affy -> gcrma->limma). 

At the first I got an error during the gcrma step:

Adjusting for optical effect....Done.
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Environment mogene10stv1probe was not found in the Bioconductor repository."
Error in get(probepackagename) : object 'mogene10stv1probe' not found


I then download the mogene10stv1probe from bioconductor 2.8 and installed the package manually & rerun the pipeline: now i am getting a new error:

> dd = gcrma(abatch)
Adjusting for optical effect....Done.
Computing affinitiesLoading required package: AnnotationDbi
Error: length(prlen) == 1 is not TRUE

I google on the error and it seem there is some problem with the probe length (instead of 25bp, some probe are 21 bp)

probepkgname ="mogene10stv1probe"
> seq = get(probepkgname)
> prlen=nchar(seq$seq)
> range(prlen)
[1] 21 25

Any idea, advice would be appreciated! ( I copied the sample code & session infor at the end of email)

Thanks a lot!
Yupu




R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0

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Type 'license()' or 'licence()' for distribution details.

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> library(gcrma)
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

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

> library(affy)
> cel.dir.zip = "/ifs/e63data/galaxy/galaxy-dist/database/files/000/dataset_396_files/rexpression.cel.zip"
> cel.dir = dirname(cel.dir.zip)
> abatch = ReadAffy(celfile.path=cel.dir) dd = gcrma(abatch)
Adjusting for optical effect....Done.
Computing affinitiesLoading required package: AnnotationDbi
Error: length(prlen) == 1 is not TRUE
> probepkgname ="mogene10stv1probe"
> seq = get(probepkgname)
> prlen=nchar(seq$seq)
> range(prlen)
[1] 21 25

> sessionInfo()
R version 2.10.0 (2009-10-26)
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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mogene10stv1probe_2.8.0 AnnotationDbi_1.14.1    mogene10stv1cdf_2.8.0 
[4] gcrma_2.18.1            affy_1.24.2             Biobase_2.6.1         

loaded via a namespace (and not attached):
[1] affyio_1.14.0        Biostrings_2.14.12   DBI_0.2-5           
[4] IRanges_1.4.16       preprocessCore_1.8.0 RSQLite_0.9-4       
[7] splines_2.10.0       tools_2.10.0    

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