[BioC] query on variance parameters for RMA

[James W. MacDonald]

Hi Hugh,

It's simple enough to get these data on a probeset-by-probeset basis:

 > library(affydata)
 > data(Dilution)
 > medpolish(log2(pm(Dilution, "1007_s_at")))
1: 5.536431
2: 4.554366
Final: 4.528792

Median Polish Results (Dataset: "log2(pm(Dilution, "1007_s_at"))")

Overall: 8.618676

Row Effects:
  1007_s_at1  1007_s_at2  1007_s_at3  1007_s_at4  1007_s_at5  1007_s_at6
-0.59973136  0.29592898  0.78257437  2.05732074  2.39466709  1.73948500
  1007_s_at7  1007_s_at8  1007_s_at9 1007_s_at10 1007_s_at11 1007_s_at12
-0.04027435 -0.06544218 -0.67467511  0.69974913  0.51478816 -0.13604974
1007_s_at13 1007_s_at14 1007_s_at15 1007_s_at16
-0.15326752 -1.90470573 -1.11026444  0.04027435

Column Effects:
        20A        20B        10A        10B
  0.5728390 -0.1144511  0.1202443 -0.6362839

Residuals:
                     20A        20B        10A         10B
1007_s_at1  -0.18749394 -0.0465129  0.0407198  0.17422802
1007_s_at2   0.13826450  0.0295685 -0.1240571 -0.03039400
1007_s_at3   0.07439714 -0.0317711  0.0259779 -0.03874874
1007_s_at4  -0.03633972  0.1518405 -0.0181643  0.01217539
1007_s_at5   0.07528392 -0.0683772  0.0625840 -0.09050186
1007_s_at6   0.00379623  0.0646288 -0.0087639 -0.11399244
1007_s_at7   0.04055849 -0.0460984 -0.0440103  0.03802140
1007_s_at8  -0.11484593  0.0062318  0.0840782 -0.00705727
1007_s_at9  -0.02900022 -0.0267107  0.1319877  0.02588521
1007_s_at10 -0.12805213  0.1904883  0.0268966 -0.03288549
1007_s_at11 -0.00067114  0.0083397 -0.1167177  0.00067114
1007_s_at12  0.02934276 -0.0062318 -0.2409272  0.00540625
1007_s_at13  0.00067114  0.0109860 -0.1899048 -0.00067114
1007_s_at14 -0.09698507 -0.0145570  0.0087639  0.07814337
1007_s_at15 -0.26554742 -0.0828937  0.1806296  0.08206822
1007_s_at16  0.03967331  0.1902100 -0.2177162 -0.03967331

And doing it on a whole array isn't that expensive:

 > pms <- pm(Dilution, LISTRUE = TRUE)
 > system.time(meds <- lapply(pms, medpolish, trace.iter=FALSE))
    user  system elapsed
  62.387   0.033  62.439

Best,

Jim



On 2/20/2013 7:39 AM, Hugh Shanahan wrote:
> Hi,
>        we would like to compute the parameters (i.e, the other parameters that are computed via the median polish algorithm) that are computed in the final summarisation step in RMA. In particular, we'd like to determine the parameter alpha_i that tells us how the estimate for the expression varies as a function of the probe. I guess it's possible to open up the relevant C-code and find it there, but are there are libraries that allow one to do it more easily ? I saw that affyPLM appears to be doing something similar - is this where we should be looking ?
>
> Many thanks,
> Hugh
>
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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