[BioC] Help on invariantset normalization function

[James W. MacDonald]

Hi Sophie,

On 7/2/2012 8:03 AM, Sophie Lamarre wrote:
> 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

When you do

data_ready_to_normalize_met1[,1]


you are selecting data from only one array. It isn't possible to figure 
out which probesets are invariant with only one array (because the 
implication is that the probesets don't vary in any array).

Is there a particular reason that you are trying to normalize just one 
array?

Best,

Jim



>
>
> # 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
>
> My session info:
>
>
>>   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
>
>
> 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
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099