problem to compute copy number with crlmm
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@soren-grottrup-3794
Last seen 10.2 years ago
Hi, I'm trying to compute the copy number for the Illumina 660W-Quad bead array with the package crlmm. But for some chromosome it doesn't work and I get the following message: > computeCopynumber(crlmmSetList) 'batch' missing. Assuming all samples in the CrlmmSetList object were processed together in the same batch. Fitting model for copy number estimation... Using 50 df for inverse chi squares. Sufficient statistics . Estimating coefficients .Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir) Browse[1]> What shall I do? When I press enter I get: Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir) : Inf values in W or V > traceback() 5: stop("Inf values in W or V") 4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir) 3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir = envir, CONF.THR = CONF.THR, MIN.OBS = MIN.OBS) 2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), calls = calls(snpset), conf = confs(snpset), NP = A(NPset), plate = batch, envir = envir, SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName = cdfName, ...) 1: computeCopynumber(crlmmSetList) What could be the problem? I'm glad for any help. Thanks in advance S?ren
GLAD crlmm GLAD crlmm • 1.7k views
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 10.2 years ago
> Hi, > I'm trying to compute the copy number for the Illumina 660W-Quad > bead array > with the package crlmm. But for some chromosome it doesn't work and > I get the > following message: > >> computeCopynumber(crlmmSetList) > 'batch' missing. Assuming all samples in the CrlmmSetList object were > processed together in the same batch. > Fitting model for copy number estimation... > Using 50 df for inverse chi squares. > Sufficient statistics > . > Estimating coefficients > .Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, > envir = > envir) > Browse[1]> > > What shall I do? When I press enter I get: > > Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir > = envir) : Benilton has removed the browser from the devel and release versions. crlmm uses the MAD as a robust estimate of the within-genotype spread of intensities on the intensity-scale. These estimates are used as weights in a regression model. What has most likely happened is that some of these estimates were zero and the inverse variances (the weights) are INF. We could replace the zeros with some constant to prevent the error and replace the stop() with a warning() message, but usually the error is a side effect of something more serious -- I would like to understand why the zero's occur in the first place. I will try to reproduce the error, but I need to know - how many samples you are processing with crlmm - your sessionInfo() Thanks, Rob > Inf values in W or V >> traceback() > 5: stop("Inf values in W or V") > 4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir) > 3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir = > envir, > CONF.THR = CONF.THR, MIN.OBS = MIN.OBS) > 2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), calls = > calls(snpset), > conf = confs(snpset), NP = A(NPset), plate = batch, envir = > envir, > SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName = > cdfName, > ...) > 1: computeCopynumber(crlmmSetList) > > > What could be the problem? I'm glad for any help. > > Thanks in advance > S?ren
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@soren-grottrup-3794
Last seen 10.2 years ago
I'm sorry. Here my sessionInfo(): > sessionInfo() R version 2.10.0 RC (2009-10-18 r50160) x86_64-pc-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] human660quadv1aCrlmm_1.0.0 crlmm_1.4.0 [3] Biobase_2.6.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.8.0 Biostrings_2.14.0 DBI_0.2-4 [4] IRanges_1.4.0 RSQLite_0.7-3 SNPchip_1.10.0 [7] affyio_1.14.0 annotate_1.24.0 ellipse_0.3-5 [10] genefilter_1.28.0 mvtnorm_0.9-8 oligoClasses_1.8.0 [13] preprocessCore_1.8.0 splines_2.10.0 survival_2.35-7 [16] tools_2.10.0 xtable_1.5-5 Vincent Carey schrieb am 2009-11-11: > be sure to send your sessionInfo() output to help with diagnosis > On Wed, Nov 11, 2009 at 5:40 AM, S?ren Gr?ttrup > <soerengroettrup at="" uni-muenster.de=""> wrote: > > Hi, > > I'm trying to compute the copy number for the Illumina 660W-Quad > > bead array > > with the package crlmm. But for some chromosome it doesn't work and > > I get the > > following message: > >> computeCopynumber(crlmmSetList) > > 'batch' missing. ?Assuming all samples in the CrlmmSetList object > > were > > processed together in the same batch. > > Fitting model for copy number estimation... > > Using 50 df for inverse chi squares. > > Sufficient statistics > > . > > Estimating coefficients > > .Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, > > envir = > > envir) > > Browse[1]> > > What shall I do? When I press enter I get: > > Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir > > = envir) : > > ?Inf values in W or V > >> traceback() > > 5: stop("Inf values in W or V") > > 4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = > > envir) > > 3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir = > > envir, > > ? ? ? CONF.THR = CONF.THR, MIN.OBS = MIN.OBS) > > 2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), > > calls = > > calls(snpset), > > ? ? ? conf = confs(snpset), NP = A(NPset), plate = batch, envir = > > envir, > > ? ? ? SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName = > > cdfName, > > ? ? ? ...) > > 1: computeCopynumber(crlmmSetList) > > What could be the problem? I'm glad for any help. > > Thanks in advance > > S?ren > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Soren, apologies for the inconvenience. I have fixed the problem and just uploaded a new version of the crlmm package to address this issua (version 1.4.1), which should be available in 1 (max 2) days. This fixes the "Browse[1]>" thing you saw. Now , regarding the error "Inf values in W or V", how many samples do you have available? Thanks a lot, b On Nov 11, 2009, at 9:31 AM, S?ren Gr?ttrup wrote: > I'm sorry. Here my sessionInfo(): > >> sessionInfo() > R version 2.10.0 RC (2009-10-18 r50160) > x86_64-pc-linux-gnu > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] human660quadv1aCrlmm_1.0.0 crlmm_1.4.0 > [3] Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.8.0 Biostrings_2.14.0 DBI_0.2-4 > [4] IRanges_1.4.0 RSQLite_0.7-3 SNPchip_1.10.0 > [7] affyio_1.14.0 annotate_1.24.0 ellipse_0.3-5 > [10] genefilter_1.28.0 mvtnorm_0.9-8 oligoClasses_1.8.0 > [13] preprocessCore_1.8.0 splines_2.10.0 survival_2.35-7 > [16] tools_2.10.0 xtable_1.5-5 > > > > > Vincent Carey schrieb am 2009-11-11: >> be sure to send your sessionInfo() output to help with diagnosis > >> On Wed, Nov 11, 2009 at 5:40 AM, S?ren Gr?ttrup >> <soerengroettrup at="" uni-muenster.de=""> wrote: >>> Hi, >>> I'm trying to compute the copy number for the Illumina 660W-Quad >>> bead array >>> with the package crlmm. But for some chromosome it doesn't work and >>> I get the >>> following message: > >>>> computeCopynumber(crlmmSetList) >>> 'batch' missing. Assuming all samples in the CrlmmSetList object >>> were >>> processed together in the same batch. >>> Fitting model for copy number estimation... >>> Using 50 df for inverse chi squares. >>> Sufficient statistics >>> . >>> Estimating coefficients >>> .Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, >>> envir = >>> envir) >>> Browse[1]> > >>> What shall I do? When I press enter I get: > >>> Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir >>> = envir) : >>> Inf values in W or V >>>> traceback() >>> 5: stop("Inf values in W or V") >>> 4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = >>> envir) >>> 3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir = >>> envir, >>> CONF.THR = CONF.THR, MIN.OBS = MIN.OBS) >>> 2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), >>> calls = >>> calls(snpset), >>> conf = confs(snpset), NP = A(NPset), plate = batch, envir = >>> envir, >>> SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName = >>> cdfName, >>> ...) >>> 1: computeCopynumber(crlmmSetList) > > >>> What could be the problem? I'm glad for any help. > >>> Thanks in advance >>> S?ren > >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks for the fast answer. I will install the new version as soon as possible. I have 12 samples available. But some of them contain the same data because I copied them to get more then 10 samples. Hope that's not a problem. S?ren Benilton Carvalho schrieb am 2009-11-11: > Dear Soren, > apologies for the inconvenience. > I have fixed the problem and just uploaded a new version of the > crlmm package to address this issua (version 1.4.1), which should > be available in 1 (max 2) days. > This fixes the "Browse[1]>" thing you saw. Now , regarding the error > "Inf values in W or V", how many samples do you have available? > Thanks a lot, > b > On Nov 11, 2009, at 9:31 AM, S?ren Gr?ttrup wrote: > >I'm sorry. Here my sessionInfo(): > >>sessionInfo() > >R version 2.10.0 RC (2009-10-18 r50160) > >x86_64-pc-linux-gnu > >locale: > >[1] C > >attached base packages: > >[1] stats graphics grDevices utils datasets methods base > >other attached packages: > >[1] human660quadv1aCrlmm_1.0.0 crlmm_1.4.0 > >[3] Biobase_2.6.0 > >loaded via a namespace (and not attached): > >[1] AnnotationDbi_1.8.0 Biostrings_2.14.0 DBI_0.2-4 > >[4] IRanges_1.4.0 RSQLite_0.7-3 SNPchip_1.10.0 > >[7] affyio_1.14.0 annotate_1.24.0 ellipse_0.3-5 > >[10] genefilter_1.28.0 mvtnorm_0.9-8 oligoClasses_1.8.0 > >[13] preprocessCore_1.8.0 splines_2.10.0 survival_2.35-7 > >[16] tools_2.10.0 xtable_1.5-5 > >Vincent Carey schrieb am 2009-11-11: > >>be sure to send your sessionInfo() output to help with diagnosis > >>On Wed, Nov 11, 2009 at 5:40 AM, S?ren Gr?ttrup > >><soerengroettrup at="" uni-muenster.de=""> wrote: > >>>Hi, > >>>I'm trying to compute the copy number for the Illumina 660W-Quad > >>>bead array > >>>with the package crlmm. But for some chromosome it doesn't work > >>>and > >>>I get the > >>>following message: > >>>>computeCopynumber(crlmmSetList) > >>>'batch' missing. Assuming all samples in the CrlmmSetList object > >>>were > >>>processed together in the same batch. > >>>Fitting model for copy number estimation... > >>>Using 50 df for inverse chi squares. > >>>Sufficient statistics > >>>. > >>>Estimating coefficients > >>>.Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, > >>>envir = > >>>envir) > >>>Browse[1]> > >>>What shall I do? When I press enter I get: > >>>Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, > >>>envir > >>>= envir) : > >>>Inf values in W or V > >>>>traceback() > >>>5: stop("Inf values in W or V") > >>>4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = > >>>envir) > >>>3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir > >>>= > >>>envir, > >>> CONF.THR = CONF.THR, MIN.OBS = MIN.OBS) > >>>2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), > >>>calls = > >>>calls(snpset), > >>> conf = confs(snpset), NP = A(NPset), plate = batch, envir = > >>>envir, > >>> SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName = > >>>cdfName, > >>> ...) > >>>1: computeCopynumber(crlmmSetList) > >>>What could be the problem? I'm glad for any help. > >>>Thanks in advance > >>>S?ren > >>>_______________________________________________ > >>>Bioconductor mailing list > >>>Bioconductor at stat.math.ethz.ch > >>>https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>Search the archives: > >>>http://news.gmane.org/gmane.science.biology.informatics.conductor > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 10.2 years ago
On Nov 12, 2009, at 6:00 AM, bioconductor-request@stat.math.ethz.ch wrote: > Message: 4 > Date: Wed, 11 Nov 2009 14:23:31 +0100 (CET) > From: S?ren Gr?ttrup <soerengroettrup@uni-muenster.de> > Subject: Re: [BioC] problem to compute copy number with crlmm > To: <bioconductor@stat.math.ethz.ch> > Message-ID: > <permail-20091111132331f0889e8400005b79-sgroe_01@message-id .uni-muenster.de=""> > > > Content-Type: text/plain; charset=iso-8859-1 > > Thanks for the fast answer. I will install the new version as soon as > possible. > > I have 12 samples available. But some of them contain the same data > because I > copied them to get more then 10 samples. Hope that's not a problem. > > S?ren Hi S?ren, Yes, this would explain zeros for the within-genotype variance and the resulting error you observed. CRLMM does not pre-compute the parameters needed to estimate copy number because of large batch effects. The best solution would be to run these samples with other samples that were processed at a similar time in the same lab. If this is not possible, an alternative is to obtain a collection of samples processed at a different time in a different lab (such as hapmap). The problem with this latter approach is that apparent alterations in copy number estimates likely reflect batch differences. The genotype estimates provided by crlmm are much more robust to batch effects than copy number estimates -- running crlmm on just your samples is perfectly fine. Getting reliable estimates of copy number for a very small number of samples is a challenging problem. Rob [[alternative HTML version deleted]]
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Hi Robert, thanks a lot for your detailed answer. You helped me a lot. Soeren > Hi S?ren, > Yes, this would explain zeros for the within-genotype variance and > the resulting error you observed. CRLMM does not pre-compute the > parameters needed to estimate copy number because of large batch > effects. The best solution would be to run these samples with > other samples that were processed at a similar time in the same > lab. If this is not possible, an alternative is to obtain a > collection of samples processed at a different time in a different > lab (such as hapmap). The problem with this latter approach is > that apparent alterations in copy number estimates likely reflect > batch differences. The genotype estimates provided by crlmm are > much more robust to batch effects than copy number estimates -- > running crlmm on just your samples is perfectly fine. Getting > reliable estimates of copy number for a very small number of > samples is a challenging problem. > Rob
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Hi Robert, I have a similar situation, regarding genotypes and CNV estimates. I have a small set of samples (29) that I have included with the CEPH CEU dataset (90 samples) to increase numbers in the initial processing, and thus hopefully robustness of the data. Do I understand you correctly in that you are advising to NOT include them, particularly for CNV estimates? In terms of identifying batch effects within the sample set, what method that you might recommend? I also have another dataset which, although considerably larger, has the added confounders of: 1. having been generated in dribs and drabs over the past 3-4 years 2. multiple chips for the same patient but taken at various times from various normal and cancerous tissues. I cant do anything about the first problem, but as I am wanting to do CNV analyses, was wondering what you or others might suggest when generating or modeling the results of CNV estimates? I am now uncertain as to the wisdom of including the CEU "reference" set in these analyses. Thoughts/comments? Cheers and thanks, al > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Robert Scharpf > Sent: 12 November 2009 13:06 > To: bioconductor at stat.math.ethz.ch; soerengroettrup at uni- muenster.de > Subject: Re: [BioC] problem to compute copy number with crlmm > > > > On Nov 12, 2009, at 6:00 AM, bioconductor-request at stat.math.ethz.ch > wrote: > > > Message: 4 > > Date: Wed, 11 Nov 2009 14:23:31 +0100 (CET) > > From: S?ren Gr?ttrup <soerengroettrup at="" uni-muenster.de=""> > > Subject: Re: [BioC] problem to compute copy number with crlmm > > To: <bioconductor at="" stat.math.ethz.ch=""> > > Message-ID: > > > > > <permail-20091111132331f0889e8400005b79-sgroe_01 at="" message-id.un=""> i-muenster.de > > > > > > > Content-Type: text/plain; charset=iso-8859-1 > > > > Thanks for the fast answer. I will install the new version > as soon as > > possible. > > > > I have 12 samples available. But some of them contain the same data > > because I > > copied them to get more then 10 samples. Hope that's not a problem. > > > > S?ren > > Hi S?ren, > > Yes, this would explain zeros for the within-genotype > variance and the > resulting error you observed. CRLMM does not pre-compute the > parameters needed to estimate copy number because of large batch > effects. The best solution would be to run these samples > with other > samples that were processed at a similar time in the same > lab. If this > is not possible, an alternative is to obtain a collection of samples > processed at a different time in a different lab (such as hapmap). > The problem with this latter approach is that apparent > alterations in > copy number estimates likely reflect batch differences. The > genotype > estimates provided by crlmm are much more robust to batch > effects than > copy number estimates -- running crlmm on just your samples is > perfectly fine. Getting reliable estimates of copy number > for a very > small number of samples is a challenging problem. > > Rob > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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