[BioC] lumi: estimateMethylationBG problem

Ina Hoeschele inah at vbi.vt.edu
Wed May 18 20:29:56 CEST 2011 

sorry for the stupid question, but how do I install the developing version of lumi 2.5.1  mentioned by Pan below?

I'm running OpenSuse 11.2 and here is the R that I have installed:

inah-960:~ # rpm -qa | grep R-
R-patched-2.13.0-33.1.x86_64
R-patched-devel-2.13.0-33.1.x86_64

When I install lumi using biocLite, it tells me this:

trying URL 'http://bioconductor.org/packages/2.8/bioc/src/contrib/lumi_2.4.0.tar.gz'

which is 2.4.0 and not 2.5.1.

Many thanks, Ina


----- Original Message -----
From: "Pan Du" <dupan.mail at gmail.com>
To: "Chao-Jen Wong" <cwon2 at fhcrc.org>
Cc: bioconductor at r-project.org
Sent: Wednesday, May 11, 2011 1:19:52 AM
Subject: Re: [BioC] lumi: estimateMethylationBG problem

Hi Chao-Jen

Because infinium 450K includes two types of probe design, I added many
updates for 450K in the developing version of lumi 2.5.1, which may fix some
of these problems. Please check it. More updates for 450K will be added in
the near future.

Thanks Tim built the annotation package!


Pan

On Tue, May 10, 2011 at 10:06 PM, Tim Triche, Jr. <tim.triche at gmail.com>wrote:

> you should have over 700 controls; you do not want to estimate background
> from only one.
>
> on the 27k arrays it is actually better to blow away the controls and not
> use them at all than to estimate background from only the 32 or so negative
> controls.  You should have over 600 negative controls on the 450k arrays,
> but if you don't, you could (at least in theory) blow them away too.  But,
> the design II probes will still be biased.  (But but, you can use the dye
> bias normalization tools to fix that problem)
>
>
>
> On Tue, May 10, 2011 at 4:47 PM, Wong, Chao-Jen <cwon2 at fhcrc.org> wrote:
>
>> Hi, Pan,
>>
>> I am working with Illumina Infinium 540K array and have problems using the
>> 'estimateMethylationBG' function from the lumi package.  Suppose
>> 'methyLumiM' is my methyLumiM instance and I got the following error
>> message:
>>
>>
>> > methyLumiM
>> MethyLumiM (storageMode: lockedEnvironment)
>> assayData: 485577 features, 24 samples
>>  element names: detection, exprs, methylated, unmethylated
>> protocolData: none
>> phenoData
>>  sampleNames: 3343-WWC-SQ 3344-WWC-NSE ... 3368-NF BE (24 total)
>>  varLabels: sampleID label sampleGroup
>>  varMetadata: labelDescription
>> featureData
>>  featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total)
>>  fvarLabels: Index TargetID ... COLOR_CHANNEL (13 total)
>>  fvarMetadata: labelDescription
>> experimentData: use 'experimentData(object)'
>> Annotation: IlluminaHumanMethylation450k
>> > estimateMethylationBG(methyLumiM)
>> Error in apply(grnData[neg.ind, ], 2, median) :
>>  dim(X) must have a positive length
>>
>>
>> I've tried to make sure that 'methyLumiM' has a controlData slot by the
>> following
>>
>> > controlData <- controlData(methyLumiM)
>> > controlData
>> MethyLumiQC (storageMode: lockedEnvironment)
>> assayData: 14 features, 24 samples
>>  element names: methylated, pvals, unmethylated
>> protocolData: none
>> phenoData: none
>> featureData
>>  featureNames: BISULFITE CONVERSION I BISULFITE CONVERSION II ...
>>    TARGET REMOVAL (14 total)
>>  fvarLabels: Index TargetID
>>  fvarMetadata: labelDescription
>> experimentData: use 'experimentData(object)'
>> Annotation:
>>
>> I read closely the code of estimateMethylationBG(), and this is what I
>> found:
>>
>> I think the problem occurs when 'featureData' instance of the
>> 'controlData' object only have one 'NEGATIVE'. For example,
>> > featureNames(controlData)
>>  [1] "BISULFITE CONVERSION I"  "BISULFITE CONVERSION II"
>>  [3] "EXTENSION"               "HYBRIDIZATION"
>>  [5] "NEGATIVE"                "NON-POLYMORPHIC"
>>  [7] "NORM_A"                  "NORM_C"
>>  [9] "NORM_G"                  "NORM_T"
>> [11] "SPECIFICITY I"           "SPECIFICITY II"
>> [13] "STAINING"                "TARGET REMOVAL"
>> > grnData <- assayDataElement(controlData, "methylated")
>> > redData <- assayDataElement(controlData, "unmethylated")
>> > allControlType <- sapply(strsplit(featureNames(controlData), "\\."),
>> function(x) x[1])
>> > allControlType <- toupper(allControlType)
>> > neg.ind <- which(allControlType == "NEGATIVE")
>> > neg.ind
>> [1] 5
>>
>> The neg.ind variable is with length of one, and this would render the
>> result of subsetting the grnData matrix to be a numeric vector:
>>
>> > grnData[neg.ind, ]
>>  3343-WWC-SQ 3344-WWC-NSE  3345-RWV-SQ 3346-RWV-NSE  3347-DAF-SQ
>> 3348-DAF-NSE
>>    276.8050     163.6250     185.8183     230.0850     407.9767
>> 459.0500
>>  3349-PEI-SQ 3350-PEI-NSE  3351-SCO-SQ 3352-SCO-NSE  3353-SRW-SQ
>> 3354-SRW-NSE
>>    260.1967     246.7550     352.0200     346.6967     483.1767
>> 535.9650
>>  3555-FAM BE  3356-FAM BE  3358-FAM BE  3359-FAM BE  3360-FAM BE  3361-FAM
>> BE
>>    238.0683     158.5200     176.8467     226.7267     247.6667
>> 265.1533
>>  3363-NF BE   3364-NF BE   3365-NF BE   3366-NF BE   3367-NF BE   3368-NF
>> BE
>>    154.0900     196.1933     184.3333     266.5150     262.8833
>> 378.9000
>>
>>
>> grnData[neg.ind, ] is no longer a matrix, and apply does not like it. This
>> cause the problem when I try to run the following line:
>>
>> > bg.grn <- apply(grnData[neg.ind, ], 2, median)
>> Error in apply(grnData[neg.ind, ], 2, median) :
>>  dim(X) must have a positive length
>>
>> I think, naively, the way to remedy it to modify the lines (603, 604 in
>> methylation_preprocessing.R) to
>>
>>                        bg.grn <- apply(grnData[neg.ind, , drop=FALSE], 2,
>> median)
>>                        bg.red <- apply(redData[neg.ind, , drop=FALSE], 2,
>> median)
>>
>> such that grnData[neg.ind, , drop=FALSE] would still be an 1-by-n matrix,
>> rather than just a vector.
>>
>> What do you think? Do you want me to send you a small subset of my
>> methyLumiM instance so that you can reproduce the error?
>>
>> Thanks,
>> Chao-Jen
>>
>>
>> > sessionInfo()
>> R version 2.13.0 Under development (unstable) (2011-02-01 r54193)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>
>> other attached packages:
>> [1] lumi_2.4.0      nleqslv_1.8     methylumi_1.8.0 Biobase_2.11.10
>>
>> loaded via a namespace (and not attached):
>>  [1] AnnotationDbi_1.13.17 DBI_0.2-5             KernSmooth_2.23-4
>>  [4] MASS_7.3-9            Matrix_0.999375-46    RSQLite_0.9-4
>>  [7] affy_1.29.2           affyio_1.19.5         annotate_1.29.2
>> [10] grid_2.13.0           hdrcde_2.15           lattice_0.19-17
>> [13] mgcv_1.7-2            nlme_3.1-97           preprocessCore_1.13.6
>> [16] tools_2.13.0          xtable_1.5-6
>> Warning message:
>> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>>
>>
>> Chao-Jen Wong
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Avenue N., M1-B514
>> PO Box 19024
>> Seattle, WA 98109
>> 206.667.4485
>> cwon2 at fhcrc.org
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> If people do not believe that mathematics is simple, it is only because
> they do not realize how complicated life is.
> John von Neumann<http://www-groups.dcs.st-and.ac.uk/%7Ehistory/Biographies/Von_Neumann.html>
>
>

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