Hi Rudy,
The "global loess" option in maNorm has a sampling component when
estimating the global loess line. The default samples 2000 points for
estimating the overall loess line. Therefore, you will observed
slight
difference in the estimation from multiple runs.
However, the difference in your data does seems to be much larger than
I
have typically encounter. This indicates that the estimated global
loess
lines from random subsets of data is very different and you may like
to
investigate the reasons for such difference. One example, is to use
"print-tip" loess and compared the difference.
If you like to turn off the sampling option and tell maNorm to use all
data in the global loess estimation, please let me know and I will
send
you the modified code.
Cheers
Jean
On Thu, 29 Nov 2007, Rudy van Eijsden wrote:
> Hi,
>
>
>
> I noticed that the maNorm function with the "loes" normalization
option from
> the marray package gives irreproducible results.
>
> When performing the maNorm function "mnorm <- maNorm(mraw,
norm="l")" on the
> same marrayRaw object twice, the results for the M-values differ:
>
>
>
> *Attempt 1:
>
>> mnorm <- maNorm(mraw, norm="l")"
>
>> mnorm at maM[1:10,1:3]
>
> Data/2006022035.txt Data/2006022036.txt Data/2006022037.txt
>
> [1,] 0.018879167 -0.021035459 0.27322552
>
> [2,] -0.179815619 0.192413729 -0.10901411
>
> [3,] 1.198385736 -1.086524647 -0.60352712
>
> [4,] -1.371507828 -0.105926648 1.70023850
>
> [5,] 3.312666352 3.995601174 -0.14438617
>
> [6,] -0.477144371 0.203647479 0.12004524
>
> [7,] -0.064336607 -0.264641717 0.27210932
>
> [8,] 0.007128637 0.086065114 0.41770312
>
> [9,] 0.052644302 0.001226107 0.52679449
>
> [10,] -0.106066947 0.205590655 -0.01910152
>
>
>
> *Attempt 2:
>
>> mnorm <- maNorm(mraw, norm="l")"
>
>> mnorm at maM[1:10,1:3]
>
> Data/2006022035.txt Data/2006022036.txt Data/2006022037.txt
>
> [1,] 0.03096721 0.03422194 0.31516138
>
> [2,] -0.22138448 0.19523012 -0.13634274
>
> [3,] 1.00893182 -1.51642222 -0.53571460
>
> [4,] -1.41207840 -0.12694801 1.67356748
>
> [5,] 2.84049228 3.15626457 -0.02876272
>
> [6,] -0.47461025 0.20277810 0.09238030
>
> [7,] -0.14826379 -0.30892746 0.23741928
>
> [8,] -0.06984206 0.04507657 0.39866073
>
> [9,] 0.06391159 0.07672604 0.56632752
>
> [10,] -0.14816946 0.20583996 -0.03607932
>
>
>
>
>
> This is de session info:
>
>> sessionInfo()
>
> R version 2.6.0 (2007-10-03)
>
> i386-pc-mingw32
>
>
>
> locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>
>
> attached base packages:
>
> [1] tools stats graphics grDevices utils datasets
methods
> base
>
>
>
> other attached packages:
>
> [1] Biobase_1.16.1 marray_1.16.0 limma_2.12.0
>
>
>
>
>
> I have also noticed the same problem on a Linux machine running the
same
> version of R and the marray package.
>
>
>
>
>
> Any suggestions?
>
>
>
>
>
> Greetings,
>
>
>
> Rudy.
>
>
>
> =================================================
> Rudy van Eijsden
>
> VIB MicroArray Facility
> Herestraat 49
> 3000 Leuven
> Post Box: 816
> Belgium
>
> e-mail:
> <mailto:rudy.vaneijsden at="" vib.be=""> Rudy.vanEijsden at vib.be
>
> web:
> <http: www.microarrays.be=""> http://www.microarrays.be
> <blocked::http: www.vib.be=""/> http://www.vib.be
>
> tel: +32 (0)16 34 79 33
> fax: +32 (0)16 34 79 40
> =================================================
>
>
>
>
> [[alternative HTML version deleted]]
>
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