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Pan Du
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@pan-du-4636
Last seen 8.1 years ago

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@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@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@fhcrc.org
>>
>> _______________________________________________
>> Bioc-devel@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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