[BioC] Inconsistent coefficient values
Richard Coulson
richard.coulson at cimr.cam.ac.uk
Mon Feb 13 18:29:59 CET 2012
Hi,
Many thanks - setting subsample to 0 seems to have fixed the problem,
though it does slow down the normalisation step a bit.
Thanks again,
Richard.
On 10/02/12 12:44, Vincent Carey wrote:
> 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 at 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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