[BioC] Help on invariantset normalization function

[Sophie LAMARRE [guest]]

Hello,

I try the invariantset normalization function (affy package) on my data:

> test_pat1 = normalize.invariantset(data_ready_to_normalize_met1[,1], bd_20hk_norm[,1], prd.td=c(0.003,0.007))
Error on while ((ns.old - ns) > 50) { : 
  missing value where TRUE / FALSE is required

# My data to normalize
data_ready_to_normalize_met1[1:5,1]
[1]  5.803779 11.566477  8.583049  8.531674  9.490483

My vector containing my 20 housekeeping genes
bd_20hk_norm[1:5,1]
[1] 14.92680 15.58281 15.15885 15.09599 15.23146


I have no missing value:
test = is.na(data_ready_to_normalize_met1[,1])
sum(test)
[1] 0
 
Could you help me or give me a example in order I can resolve my problem?

Thank your very much,

Kind Regards,

Sophie LAMARRE 

 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8       
 [4] LC_COLLATE=fr_FR.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] affy_1.32.1           preprocessCore_1.16.0 gplots_2.10.1         KernSmooth_2.23-7    
 [5] caTools_1.13          bitops_1.0-4.1        gdata_2.8.2           gtools_2.6.2         
 [9] geneplotter_1.32.1    lattice_0.20-0        annotate_1.32.3       AnnotationDbi_1.16.19
[13] Biobase_2.14.0        limma_3.10.3         

loaded via a namespace (and not attached):
[1] affyio_1.22.0       BiocInstaller_1.2.1 DBI_0.2-5           IRanges_1.12.6     
[5] RColorBrewer_1.0-5  RSQLite_0.11.1      tools_2.14.1        xtable_1.7-0       
[9] zlibbioc_1.0.1     



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