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@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@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@vib.be> Rudy.vanEijsden@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
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