[BioC] Inconsistent coefficient values

Wolfgang Huber whuber at embl.de
Fri Feb 10 18:31:17 CET 2012


Hi Richard

Vince is spot on. Do you have a reason to worry that the differences in 
results are non-negligible?

	Best wishes
	Wolfgang



Vincent Carey scripsit 02/10/2012 01:44 PM:
> 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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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber



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