[BioC] PM values for probes in a probeset: background corrected and normalized, but not summarized?

James W. MacDonald jmacdon at med.umich.edu
Mon Sep 27 21:56:23 CEST 2010


Hi Galina,

On 9/27/2010 3:24 PM, Glazko, Galina wrote:
> Dear list,
>
> I am wondering, is it possible to get Affy PM values for probes in a probeset,
> which will be background corrected and normalized, but not summarized?
>
> I know that I can get just intensities of probes, but do not know whether it is possible to
> do for them all steps - backgound correction and normalization, but without summarization.
>
> I would appreciate if someone could clarify this for me!

An example:

 > library(affydata)
 > data(Dilution)
 > abatch <- bg.correct(Dilution, "rma")
 > abatch <- normalize(abatch, "quantiles")
 > pm(abatch, "1007_s_at")
                    20A        20B        10A        10B
1007_s_at1   158.82305  160.04805  184.92305  199.94805
1007_s_at2   479.42305  399.03555  370.37305  382.37305
1007_s_at3   670.62305  570.12305  625.69805  571.37305
1007_s_at4  1619.72305 1764.99805 1566.96055 1564.28555
1007_s_at5  2264.32305 1931.99805 2094.32305 1845.04805
1007_s_at6  1313.32305 1295.56055 1258.89805 1142.59805
1007_s_at7   334.57305  278.37305  293.79805  301.54805
1007_s_at8   285.17305  285.77305  322.57305  282.87305
1007_s_at9   173.07305  150.98555  188.07305  157.44805
1007_s_at10  534.62305  638.42305  587.42305  538.02305
1007_s_at11  510.99805  471.69805  450.42305  473.49805
1007_s_at12  304.42305  264.67305  222.37305  267.27305
1007_s_at13  292.27305  264.67305  229.87305  261.94805
1007_s_at14   21.67983   18.39805   17.99024   13.83471
1007_s_at15   77.57305   82.24805  122.37305   97.42305
1007_s_at16  358.57305  368.24805  269.74805  302.42305
 > pm(Dilution, "1007_s_at")
                20A    20B    10A    10B
1007_s_at1   338.8  232.0  290.0  188.3
1007_s_at2   790.0  455.0  481.3  304.0
1007_s_at3  1059.0  611.0  748.3  423.5
1007_s_at4  2373.0 1679.0 1756.0 1061.5
1007_s_at5  3239.3 1821.0 2346.3 1249.0
1007_s_at6  1957.5 1268.0 1418.0  780.3
1007_s_at7   584.8  342.0  403.0  252.5
1007_s_at8   516.0  348.5  432.8  240.5
1007_s_at9   359.0  223.3  293.3  161.3
1007_s_at10  869.0  673.0  707.0  401.5
1007_s_at11  835.0  521.8  563.0  361.5
1007_s_at12  543.0  329.0  329.0  231.0
1007_s_at13  526.0  329.0  336.8  227.3
1007_s_at14  146.0   96.0  114.8   71.3
1007_s_at15  225.3  158.8  224.3  124.0
1007_s_at16  618.0  426.0  377.8  253.0

Best,

Jim



>
> thank you!
> Best regards
> Galina
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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