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=""> > > [[alternative HTML version deleted]]

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@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=""> > > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor