[BioC] memory problem
Sean Davis
sdavis2 at mail.nih.gov
Thu Jun 16 21:27:19 CEST 2011
On Thu, Jun 16, 2011 at 3:23 PM, Harris A. Jaffee <hj at jhu.edu> wrote:
> Where is it a replacement? Her input and output were different:
>
> batch2Meth.colQ
>
> batch2Meth.colQ.bg
>
> If you meant this code inside the function:
>
> if (method == "bgAdjust2C") {
> methyLumiM <- bgAdjustMethylation(methyLumiM,
> separateColor = separateColor,
> ...)
> }
> ........
> methyLumiM <- estimateM(methyLumiM)
>
> these are new copies, but I don't think you meant these.
Thanks, Harris. You are definitely correct in your assumption. I
meant Ina's code and misread her variable names.
Sean
> On Jun 16, 2011, at 2:52 PM, Sean Davis wrote:
>
>> 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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>>
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