[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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