[BioC] memory problem

[Sean Davis]

On Thu, Jun 16, 2011 at 2:29 PM, Ina Hoeschele <inah at vbi.vt.edu> wrote:
> 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

Yes.  Looks like you are out-of-memory.  Make sure that you are using
a clean workspace (ls()), so remove anything that you think you do not
need.  You are showing a "replacement" operation, but R doesn't do
that in-place; instead it makes a copy and then replaces the original.

Just out of curiosity, how much memory does the machine have?

Sean

> 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)
>
> 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] 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).
>
>
> Pan
>
>
> 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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