[BioC] Help needed with CopyNumber analysis for Affymetrix 250K arrays

[Christian.Stratowa at vie.boehringer-ingelheim.com]

Dear Vincent

Updating to oligo_1.3.7 and pd.mapping_0.4.1 did not help.
I get the same error as before which I can repeat with justCRLMM:

> crlmmOut <- crlmm(snprmaResults, correctionFile="outputEM.rda")
M correction not provided. Calculating. Will take several minutes.
Fitting mixture model to 3 arrays. Epsilon must reach 50.
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: String or BLOB exceeded size limit)

> tmp <- justCRLMM(cels, phenoData=pheno, batch_size=58960)
Normalization: 100.00 percent done.
Genotyping: 000.00 percent done.Error in sqliteExecStatement(con, statement,
bind.data) : 
  RS-DBI driver: (error in statement: String or BLOB exceeded size limit)

> sessionInfo()
R version 2.6.1 (2007-11-26) 
x86_64-unknown-linux-gnu 

locale:
C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] pd.mapping50k.xba240_0.4.1 oligo_1.3.7               
[3] oligoClasses_1.1.10        affxparser_1.10.1         
[5] AnnotationDbi_1.0.6        preprocessCore_1.0.0      
[7] RSQLite_0.6-4              DBI_0.2-4                 
[9] Biobase_1.16.1            

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

Best regards
Christian

==============================================
Christian Stratowa, PhD
Boehringer Ingelheim Austria
Dept NCE Lead Discovery - Bioinformatics
Dr. Boehringergasse 5-11
A-1121 Vienna, Austria
Tel.: ++43-1-80105-2470
Fax: ++43-1-80105-2782
email: christian.stratowa at vie.boehringer-ingelheim.com



-----Original Message-----
From: Vincent Carey 525-2265 [mailto:stvjc at channing.harvard.edu] 
Sent: Monday, February 04, 2008 6:33 PM
To: Stratowa,Dr.,Christian FEX BIG-AT-V
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Help needed with CopyNumber analysis for Affymetrix 250K
arrays


>
> However, the following results in an error:
> > snprma250 <- justSNPRMA(cels250, phenoData=pheno250) crlmmOut250 <- 
> > crlmm(snprma250, correctionFile="outputEM.rda")
> see: 
> https://stat.ethz.ch/pipermail/bioconductor/attachments/20080128/50495
> 06c/att
> achment.pl

Can you put a sessionInfo() for the problem with this current computation?
The pd.mapping package versions are up to 0.4.1 in devel, and i think you
need to use them.

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