As Gordon says, you cannot expect the exact same numerical answers on different platforms. Having said that, these differences seems larger than I would expect. If I was the author, I would inspect this a bit more, but I would require a completely reproducible script + data. Last time I had an issue like this (in bumphunter) it was caused by what I can only describe as a really unexpected bug, where I learned something useful. Kasper On Wed, Feb 5, 2014 at 5:58 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > This is not to with limma. To get the linear model coefficients, limma > calls lm.fit() from the stats package. > > The fact is that not all of the underlying numerical routines in R give > exactly the same results on different computer architectures. The > difference is so small that it doesn't seem a serious problem to me. > > Indeed, it could be that your numbers are already different before they > are input to limma. Have you checked that? > > Gordon > > > Date: Tue, 4 Feb 2014 14:49:42 -0800 (PST) >> From: "Pavel Fedotov [guest]" <guest@bioconductor.org> >> To: bioconductor@r-project.org, pavelph@ya.ru >> Subject: [BioC] limma lmFit returns different results on different >> computers >> >> >> I run the same program code on my laptop and on server and got different >> results. I found that the problem occured when I run >> lmFit(). I output parameters for this function and they are same on both >> computers, but result differs. >> Here is fragment of my code: >> ... >> group_names <- rep("0",length(clusters)) >> group_names[which(clusters %in% g)] <- "CT1" >> group_names[which(!(clusters %in% g))] <- "Other" >> names(group_names) <- group_names >> group_names <- factor(group_names) >> >> expr_matrix <- if (!is_log) { >> log2(expr) # do log transformation >> } else { >> expr >> } >> >> design <- model.matrix(~0+group_names) >> colnames(design) <- levels(group_names) >> colnames(expr_matrix) <- group_names >> >> print(design) >> print(head(expr_matrix)) >> print(tail(expr_matrix)) >> >> fit <- lmFit(expr_matrix, design) >> >> print(head(fit)) >> >> Last command returns me on laptop: >> >> An object of class "MArrayLM" >> $coefficients >> CT1 Other >> 226151_x_at 9.798801 9.317917 >> 1552701_a_at 8.681497 8.624071 >> 1554471_a_at 8.966830 8.452752 >> 224703_at 9.652549 9.558388 >> 202106_at 9.139795 8.852839 >> 218515_at 10.088242 10.116507 >> >> and on server: >> >> An object of class "MArrayLM" >> $coefficients >> CT1 Other >> 226151_x_at 9.798801 9.317231 >> 1552701_a_at 8.681497 8.624118 >> 1554471_a_at 8.966830 8.472994 >> 224703_at 9.652549 9.558388 >> 202106_at 9.139795 8.869085 >> 218515_at 10.088242 10.116605 >> >> Second collumn is slightly different in this cases. >> I thought that I had different versions of limma package but >> sessionInfo() shows me that all attached packages are similiar including >> limma (limma_3.18.10). >> >> Any thoughts what could it be? >> >> -- output of sessionInfo(): >> >> laptop: >> >>> sessionInfo() >>> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C >> LC_TIME=ru_RU.UTF-8 LC_COLLATE=ru_RU.UTF-8 >> LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 >> [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] compiler parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] corpcor_1.6.6 preprocessCore_1.24.0 limma_3.18.10 >> BiocInstaller_1.12.0 CellMix_1.6.1 GSEABase_1.24.0 >> graph_1.40.1 >> [8] annotate_1.40.0 AnnotationDbi_1.24.0 stringr_0.6.2 >> csSAM_1.2.4 NMF_0.20 cluster_1.14.4 >> rngtools_1.2.3 >> [15] pkgmaker_0.17.4 registry_0.2 Biobase_2.22.0 >> BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] beeswarm_0.1.6 bibtex_0.3-6 codetools_0.2-8 >> colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 >> doParallel_1.0.6 foreach_1.4.1 >> [10] genefilter_1.44.0 ggplot2_0.9.3.1 grid_3.0.2 >> gridBase_0.4-6 gtable_0.1.2 gtools_3.2.1 IRanges_1.20.6 >> iterators_1.0.6 labeling_0.2 >> [19] limSolve_1.5.5 lpSolve_5.6.7 MASS_7.3-29 >> matrixStats_0.8.14 munsell_0.4.2 plyr_1.8 proto_0.3-10 >> quadprog_1.5-5 RColorBrewer_1.0-5 >> [28] reshape2_1.2.2 R.methodsS3_1.6.1 RSQLite_0.11.4 >> scales_0.2.3 splines_3.0.2 stats4_3.0.2 survival_2.37-7 >> tools_3.0.2 XML_3.98-1.1 >> [37] xtable_1.7-1 >> >> server: >> >>> sessionInfo() >>> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=ru_RU.UTF-8 LC_COLLATE=ru_RU.UTF-8 >> [5] LC_MONETARY=ru_RU.UTF-8 LC_MESSAGES=ru_RU.UTF-8 >> [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] compiler parallel stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] corpcor_1.6.6 preprocessCore_1.24.0 limma_3.18.10 >> [4] CellMix_1.6.1 GSEABase_1.24.0 graph_1.40.1 >> [7] annotate_1.40.0 AnnotationDbi_1.24.0 stringr_0.6.2 >> [10] csSAM_1.2.4 NMF_0.20 cluster_1.14.4 >> [13] rngtools_1.2.3 pkgmaker_0.17.4 registry_0.2 >> [16] Biobase_2.22.0 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] beeswarm_0.1.6 bibtex_0.3-6 BiocInstaller_1.12.0 >> [4] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> [7] dichromat_2.0-0 digest_0.6.4 doParallel_1.0.6 >> [10] foreach_1.4.1 genefilter_1.44.0 ggplot2_0.9.3.1 >> [13] grid_3.0.2 gridBase_0.4-6 gtable_0.1.2 >> [16] gtools_3.2.1 IRanges_1.20.6 iterators_1.0.6 >> [19] labeling_0.2 limSolve_1.5.5 lpSolve_5.6.7 >> [22] MASS_7.3-29 matrixStats_0.8.14 munsell_0.4.2 >> [25] plyr_1.8 proto_0.3-10 quadprog_1.5-5 >> [28] R.methodsS3_1.6.1 RColorBrewer_1.0-5 reshape2_1.2.2 >> [31] RSQLite_0.11.4 scales_0.2.3 splines_3.0.2 >> [34] stats4_3.0.2 survival_2.37-7 tools_3.0.2 >> [37] XML_3.98-1.1 xtable_1.7-1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:13}}