[BioC] limma lmFit returns different results on different computers

Tue Feb 4 23:49:42 CET 2014

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 

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