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
--
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