memory problem

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Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

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 >>> >>> _______________________________________________ >>> 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 >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 > >

Normalization lumi methylumi Normalization lumi methylumi • 1.2k views

ADD COMMENT • link updated 13.5 years ago by Ina Hoeschele ▴ 620 • written 13.5 years ago by Sean Davis 21k

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Ina Hoeschele ▴ 620

@ina-hoeschele-2992

Last seen 3.3 years ago

United States

yes, thanks ... with enough rm()'s I got through ... ----- Original Message ----- From: "Sean Davis" <sdavis2@mail.nih.gov> To: "Harris A. Jaffee" <hj at="" jhu.edu=""> Cc: bioconductor at r-project.org Sent: Thursday, June 16, 2011 3:27:19 PM Subject: Re: [BioC] memory problem 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 >>> >>> _______________________________________________ >>> 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 >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 > > _______________________________________________ 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

ADD COMMENT • link 13.5 years ago Ina Hoeschele ▴ 620

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try this, I use it all the time (lsos() then rm() a bunch of the offending objects... helps a lot with the 450k data) .ls.objects <- function(pos=1,pattern,order.by ,decreasing=FALSE,head=FALSE,n=5){ napply <- function(names, fn) sapply(names, function(x) fn(get(x, pos = pos))) names <- ls(pos = pos, pattern = pattern) obj.class <- napply(names, function(x) as.character(class(x))[1]) obj.mode <- napply(names, mode) obj.type <- ifelseis.na(obj.class), obj.mode, obj.class) obj.size <- napply(names, object.size) obj.dim <- t(napply(names, function(x) as.numeric(dim(x))[1:2])) vec <- is.na(obj.dim)[, 1] & (obj.type != "function") obj.dim[vec, 1] <- napply(names, length)[vec] out <- data.frame(obj.type, obj.size, obj.dim) names(out) <- c("Type", "Size", "Rows", "Columns") if (!missingorder.by)) out <- out[order(out[[order.by]], decreasing=decreasing), ] if (head) out <- head(out, n) out } lsos <- function(..., n=10) { .ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n) } On Thu, Jun 16, 2011 at 12:49 PM, Ina Hoeschele <inah@vbi.vt.edu> wrote: > yes, thanks ... with enough rm()'s I got through ... > > ----- Original Message ----- > From: "Sean Davis" <sdavis2@mail.nih.gov> > To: "Harris A. Jaffee" <hj@jhu.edu> > Cc: bioconductor@r-project.org > Sent: Thursday, June 16, 2011 3:27:19 PM > Subject: Re: [BioC] memory problem > > On Thu, Jun 16, 2011 at 3:23 PM, Harris A. Jaffee <hj@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@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@vbi.vt.edu> > >>> To: "Pan Du" <dupan.mail@gmail.com> > >>> Cc: bioconductor@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@gmail.com> > >>> To: "Ina Hoeschele" <inah@vbi.vt.edu>, "Tim Rayner" > >>> <tfrayner@gmail.com>, bioconductor@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@vbi.vt.edu> > >>> To: Tim Rayner <tfrayner@gmail.com> > >>> Cc: Bioconductor <bioconductor@stat.math.ethz.ch> > >>> Subject: Re: [BioC] lumi, Illumina Methylation 450k, and robust > >>> methylation calls > >>> Message-ID: <9267536a-70f6-4582-a38f- > >>> 8d2288c2afed@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 > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/ > >>> gmane.science.biology.informatics.conductor > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/ > >>> gmane.science.biology.informatics.conductor > >>> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/ > >> gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]

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