[BioC] limma lmFit returns different results on different computers
Gordon K Smyth
smyth at wehi.EDU.AU
Wed Feb 5 23:58:43 CET 2014
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 at bioconductor.org>
> To: bioconductor at r-project.org, pavelph at 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 intend...{{dropped:4}}
More information about the Bioconductor
mailing list