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Gabriel Wajnberg
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60
@gabriel-wajnberg-5240
Last seen 10.3 years ago
I'm testing RINGO on an agilent chip on chip array with this geo
sample:
[1]http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9267
Well, i've already understood something about the data, for example
there
are two different chips, one with probes for chromosomes 1 to 10
and other
for chromosomes 11 to X and Y.
So I 've got this RG vector... where $R are methilated signals and
$G are
genomic dna control.... and we have samples using wild type
cells (
array1_wt) and double knockouts cells (array2_dko), I would like to
process
it , normalize intensities....
when I try preprocess this what happens:
> X <- preprocess(RG[RG$genes$ControlT==0,])
Error: idColumn %in% names(myRG$genes) is not TRUE
so what do I do ? How can I preprocess and normalize the data?
thanks
> show(RG)
Loading required package: limma
An object of class "RGList"
$G
array1_dko array1_wt
[1,] 291.53850 339.50000
[2,] 78.48148 90.24138
[3,] 89.00000 98.46154
[4,] 387.67860 455.17240
[5,] 718.86670 749.81480
41915 more rows ...
$Gb
array1_dko array1_wt
[1,] 54 54
[2,] 54 54
[3,] 54 54
[4,] 56 54
[5,] 54 54
41915 more rows ...
$R
array1_dko array1_wt
[1,] 426.6538 446.3846
[2,] 82.7037 101.9655
[3,] 102.4333 113.1538
[4,] 554.7857 665.8276
[5,] 1108.6670 1008.6670
41915 more rows ...
$Rb
array1_dko array1_wt
[1,] 71 70
[2,] 70 70
[3,] 71 70
[4,] 70 69
[5,] 72 69
41915 more rows ...
$targets
FileName
array1_dko array1_dko.txt
array1_wt array1_wt.txt
$genes
Row Col ProbeUID ControlType ProbeName GeneName
1 1 1 0 1 BrightCorner BrightCorner
2 1 2 1 -1 (-)3xSLv1 NegativeControl
3 1 3 2 0 A_76_P0137287 OCM
4 1 4 4 0 A_76_P0137107 DEC1
5 1 5 6 0 A_76_P0136934 LSM6
SystematicName Description
1 BrightCorner
2 NegativeControl
3 chr7:97264626-97264686 PROMOTER
4 chr9:114982789-114982849 PROMOTER
5 chr4:147454740-147454800 INSIDE
41915 more rows ...
$source
[1] "agilent"
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Gabriel Wajnberg
Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo
Cruz -
Fiocruz - RJ
Laborat??rio de Bioinform??tica e Biologia Computacional (LBBC)
Coordena????o de Pesquisa (CPQ)
Instituto Nacional de C??ncer (INCA)
Rio de Janeiro - RJ
Tel: (21) 3207-6546
Cel: (21) 9313-2160
References
1. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9267
