Error in gammaFitEM for library(lumi) [Possible Bug]
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@chang-jun-park-5086
Last seen 6.8 years ago
Dear Bioconductor developers, My name is Chris Park who is working as a bioinformatician in University Health Network in Toronto. I'm currently working with Illumina methylation data by preprocessing them in R, and discovered a problem in which it could potentially be a bug. The bug happens when I call function for Methylation calls: lumiMethyStatus {lumi}, which gives this error message: Error in if (truncate) { : argument is not interpretable as logical > traceback() 3: gammaFitEM(x, ...) 2: methylationCall(M[, i], ...) 1: lumiMethyStatus(data.lumiMethy.bc.adj.quantile[, c(1:8)]) As shown on traceback(), the error is in gammaFitEM. After looking at the code, I found that if iteration reaches the maxInteration (hard-coded as 50), it will enter: 1 if (iter == maxIteration) { 2 Mode <- c(s[1] + (k[1] - 1) * theta[1], s[2] - (k[2] - 3 1) * theta[2]) 4 f1 <- dgamma(x - s[1], shape = k[1], scale = theta[1]) 5 f2 <- dgamma(s[2] - x, shape = k[2], scale = theta[2]) 6 if (truncate) { 7 f1 <- f1/(pgamma(Mode[2] - s[1], shape = k[1], scale = theta[1], 8 lower.tail = TRUE)) 9 f2 <- f2/(pgamma(s[2] - Mode[1], shape = k[2], scale = theta[2], 10 lower.tail = TRUE)) 11 z1 <- p[1] * f1/(p[1] * f1 + p[2] * f2) 12 z1[x > Mode[2]] <- 0 13 z1[x < Mode[1]] <- 1 14 f1[x > Mode[2]] <- 0 15 f2[x < Mode[1]] <- 0 16 } 17 else { 18 z1 <- p[1] * f1/(p[1] * f1 + p[2] * f2) 19 } 20 z2 <- 1 - z1 21 } Where on line 6, it checks for logical argument: truncate, but this logical variable is nowhere to be found. What do you suggest is the best solution is? Theoretically, what is a reason to decide whether to "truncate" or not when we reach maximum iteration of the "while" loop? I am using the latest R version available with the most recent package, as shown in sessionInfo(): > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KernSmooth_2.23-7 IlluminaHumanMethylation450k.db_1.4.6 [3] org.Hs.eg.db_2.6.4 RSQLite_0.11.1 [5] DBI_0.2-5 AnnotationDbi_1.16.11 [7] lumi_2.6.0 nleqslv_1.9.2 [9] methylumi_2.0.4 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.1 [4] BiocInstaller_1.2.1 grid_2.14.1 hdrcde_2.15 [7] IRanges_1.12.5 lattice_0.20-0 MASS_7.3-16 [10] Matrix_1.0-3 mgcv_1.7-13 nlme_3.1-103 [13] preprocessCore_1.16.0 tools_2.14.1 xtable_1.6-0 [16] zlibbioc_1.0.0 [[alternative HTML version deleted]]
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@elodie-chapeaublanc-4525
Last seen 6.8 years ago
Hello, I have the same problem with my own Illumina Methylation 27k data. This error doesn't appear with example.lumiMeth object. Do you have any solution ? Thanks, Elodie
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Pan Du ▴ 440
@pan-du-4636
Last seen 6.8 years ago
Thanks! Elodie It's a bug after I updated the code last time. I have fixed it by adding an additional parameter "truncate=FALSE" to the gammaFitEM function. I will upload the change together with many other methylation related updates at the end of this week. Pan > Subject: Re: [BioC] Error in gammaFitEM for library(lumi) [Possible Bug] > Date: Tue, 14 Feb 2012 08:23:57 +0000 > From: Elodie Chapeaublanc <elodie.chapeaublanc at="" curie.fr=""> > To: <bioconductor at="" stat.math.ethz.ch=""> > > Hello, > My name is Elodie Chapeaublanc. I am a Bioinformatician in Institute CURIE at Paris. > I want to use lumi package in order to preprocess Illumina methylation 27K data. > When I try to use lumiMethyStatus on matrix data, an error appear : > Error in if (truncate) { : argument is not interpretable as logical > I haven't got error with example.lumiMethy object. > How can I resolve this error? > Thanks, > Elodie
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