I believe you need to have a look at the documentation of vsn2

subsample: Integer of length 1. If its value is greater than 0, the
          model parameters are estimated from a subsample of the data
          of size 'subsample' only, yet the fitted transformation is
          then applied to all data. For large datasets, this can
          substantially reduce the CPU time and memory consumption at a
          negligible loss of precision. Note that the 'AffyBatch'
          method of 'vsn2' sets a value of '30000' for this parameter
          if it is missing from the function call - which is different
          from the behaviour of the other methods.


On Fri, Feb 10, 2012 at 5:22 AM, Richard Coulson [guest] <
guest@bioconductor.org> wrote:

>
> Hi,
>
> I have a problem with using 'limma' when I'm analysing some microarray
> data. If I run the below code WITHOUT setting a seed, I get slightly
> different values for the coefficients each time it's run; however this
> problem does not occur if I do set one (e.g. set.seed(1223762671)) :-
>
> raw.data <-ReadAffy( celfile.path="CEL directory" )
> normalised.data <-vsnrma(raw.data)
>
> transfect.lmFit <-lmFit( normalised.data, design.matrix )
> cont.lmFit <-contrasts.fit(transfect.lmFit, cont.matrix)
>
> i.e. the values in cont.lmFit$coefficients are altered from one R session
> to another.
>
> Please could anyone help with this?
>
> Many thanks,
> Richard.
>
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hugene11stv1cdf_1.26.0 limma_3.4.4            vsn_3.16.0
> [4] affyPLM_1.24.0         preprocessCore_1.10.0  gcrma_2.20.0
> [7] affy_1.26.1            Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0     Biostrings_2.16.9 grid_2.12.2       IRanges_1.6.8
> [5] lattice_0.19-17   splines_2.12.2    tools_2.12.2
>
> > cont.matrix
>                 Contrasts
> Levels            (C.GFP.24+C.GFP.48+C.GFP.72)-(mock.24+mock.48+mock.72)
>  C.GFP.24                                                             1
>  C.GFP.48                                                             1
>  C.GFP.72                                                             1
>  mock.24                                                             -1
>  mock.48                                                             -1
>  mock.72                                                             -1
>  myc.24                                                               0
>  myc.48                                                               0
>  myc.72                                                               0
>  N.GFP.24                                                             0
>  N.GFP.48                                                             0
>  N.GFP.72                                                             0
>  untransfected.0                                                      0
>                 Contrasts
> Levels            (N.GFP.24+N.GFP.48+N.GFP.72)-(mock.24+mock.48+mock.72)
>  C.GFP.24                                                             0
>  C.GFP.48                                                             0
>  C.GFP.72                                                             0
>  mock.24                                                             -1
>  mock.48                                                             -1
>  mock.72                                                             -1
>  myc.24                                                               0
>  myc.48                                                               0
>  myc.72                                                               0
>  N.GFP.24                                                             1
>  N.GFP.48                                                             1
>  N.GFP.72                                                             1
>  untransfected.0                                                      0
>                 Contrasts
> Levels            (myc.24+myc.48+myc.72)-(mock.24+mock.48+mock.72)
>  C.GFP.24                                                       0
>  C.GFP.48                                                       0
>  C.GFP.72                                                       0
>  mock.24                                                       -1
>  mock.48                                                       -1
>  mock.72                                                       -1
>  myc.24                                                         1
>  myc.48                                                         1
>  myc.72                                                         1
>  N.GFP.24                                                       0
>  N.GFP.48                                                       0
>  N.GFP.72                                                       0
>  untransfected.0                                                0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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