[BioC] memory problem

Ina Hoeschele inah at vbi.vt.edu
Thu Jun 16 20:29:54 CEST 2011

Hi all,
  I'm running the methlumiB function in the lumi package on a Methylumi object of 8 450K meth bead chips - all it should be doing is to subtract the median intensity of my negative control data, but I am getting the error message below
> batch2Meth.colQ.bg <- lumiMethyB(batch2Meth.colQ,method="bgAdjust2C",separateColor=F)
Perform bgAdjust2C background correction ...
Error: cannot allocate vector of size 355.6 Mb

Does anyone have a hint for me (this is not hardware limitation!)?

Thanks, Ina

> sessionInfo()
R version 2.14.0 Under development (unstable) (2011-05-19 r55967)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] affy_1.31.1                           lattice_0.19-26                      
 [3] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.5.0                   
 [5] RSQLite_0.9-4                         DBI_0.2-5                            
 [7] AnnotationDbi_1.15.3                  lumi_2.5.1                           
 [9] nleqslv_1.8.5                         methylumi_1.9.0                      
[11] Biobase_2.13.2                       

loaded via a namespace (and not attached):
 [1] affyio_1.21.1         annotate_1.31.0       grid_2.14.0          
 [4] hdrcde_2.15           KernSmooth_2.23-5     MASS_7.3-13          
 [7] Matrix_0.999375-50    mgcv_1.7-6            nlme_3.1-101         
[10] preprocessCore_1.15.0 tools_2.14.0          xtable_1.5-6         

----- Original Message -----
From: "Ina Hoeschele" <inah at vbi.vt.edu>
To: "Pan Du" <dupan.mail at gmail.com>
Cc: bioconductor at r-project.org
Sent: Wednesday, June 15, 2011 4:40:41 PM
Subject: Re: [BioC] lumi, Illumina Methylation 450k,	and robust methylation calls

thank you very much, Pan, so the color adjustment makes perfect sense to me now. Now for the background correction, lumi subtracts the median intensity of the negative control probes, while GenomeStudio subtracts the 5th percentile - does anyone know why?
Thanks again, Ina

----- Original Message -----
From: "Pan Du" <dupan.mail at gmail.com>
To: "Ina Hoeschele" <inah at vbi.vt.edu>, "Tim Rayner" <tfrayner at gmail.com>, bioconductor at r-project.org
Sent: Tuesday, June 14, 2011 11:34:27 AM
Subject: Re: [BioC] lumi, Illumina Methylation 450k, and robust methylation calls

Hi Ina and Tim

For the methylation call part, I haven't work on that for a while because
there are other priorities.

For the color bias adjustment of 450K array, you need to use the development
version, which perform color bias adjustment for both type I and II designs.
Basically, it estimates the color bias based on type I design (methylated
and unmenthylated measurements of the same CpG-site has  the same color),
which is the same as Infinium 27k, and then use the fitted curve to adjust
probes with type II design (methylated and unmenthylated measurements of the
same CpG-site has different colors).


Date: Mon, 13 Jun 2011 18:05:16 -0400
From: Ina Hoeschele <inah at vbi.vt.edu>
To: Tim Rayner <tfrayner at gmail.com>
Cc: Bioconductor <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] lumi, Illumina Methylation 450k,    and robust
       methylation calls
Message-ID: <9267536a-70f6-4582-a38f-
8d2288c2afed at zimbra>
Content-Type: text/plain; charset="utf-8"

I have recently started to use the lumi package to analyse some
Illumina Human Methylation 450k data, and I have run into some
problems which seem to revolve around division by zero in the
gammaFitEM() function. I have adjusted the colour balance and quantile
normalised as suggested in the vignette

Hi Pan and Tim (et al),
  this is in regard to an earlier email from Tim - is the colour balance
adjustment performed for ALL probes or only for probes with Infinium I
assay? Is the quantile normalization done for both Inf I and II together
(rather than separately) in the current (development) version of lumi? I
would be reluctant to do it that way, and I apologize if this is described
somewhere and I misssed this informaiton.
Thanks, Ina

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