Use the 'prcomp' function rather than 'princomp'. The help page for 'princomp' refers to 'prcomp' a couple of times, the last paragraph in the details section says that 'princomp' requires "at least as many units as variables", then points to 'prcomp' as using the alternative method (which does not require more observations than variables).
On Thu, Sep 12, 2013 at 8:31 AM, Hermann Norpois <hnorp...@gmail.com> wrote: > Hello, > > I would like to do a pca with princomp. > > I have a dataset with different observations for each row and for different > variables for each column (test.z). If I understood it correctly this is > the way the data should be structured for princomp. But it does not work. > But if I transpose the matrix (test.t - see below) it works. > > > test.z[1:3,1:6] > rs1291584 rs3737728 rs6687776 rs9651273 rs4970405 rs12726255 > 1 1.058438 3.175315 -3.704534 -3.439924 -2.116876 -2.381486 > 2 -6.879848 -4.762972 4.233753 -3.439924 -2.116876 -2.381486 > 3 -6.879848 -4.762972 4.233753 -3.439924 -2.116876 -2.381486 > > prc <- princomp (test.z) > Fehler in princomp.default(test.z) : > 'princomp' kann nur mit mehr Einheiten als Variablen genutzt werden > > After tranposing the matrix - it works. > Transposed matrix: > > test.t <- t (test.z) > > prc <- princomp (test.t) > > prc > Call: > princomp(x = test.t) etc > > The error message might give the answer: I understand it like this: You > need more obsvervations than variables. Does this make sense? > > Thanks for some hints > hermann > > > dput (test.z) > structure(c(1.05843820744527, -6.87984834839428, -6.87984834839428, > -6.87984834839428, 8.99672476328483, 8.99672476328483, -6.87984834839428, > 8.99672476328483, -6.87984834839428, -6.87984834839428, 1.05843820744527, > -6.87984834839428, 8.99672476328483, 1.05843820744527, 1.05843820744527, > -6.87984834839428, -6.87984834839428, 8.99672476328483, 1.05843820744527, > 8.99672476328483, 1.05843820744527, -6.87984834839428, 1.05843820744527, > 1.05843820744527, 8.99672476328483, 1.05843820744527, 8.99672476328483, > 1.05843820744527, -6.87984834839428, -6.87984834839428, 3.17531462233582, > -4.76297193350373, -4.76297193350373, 3.17531462233582, -4.76297193350373, > -4.76297193350373, 3.17531462233582, -4.76297193350373, 3.17531462233582, > -4.76297193350373, -4.76297193350373, -4.76297193350373, 3.17531462233582, > 3.17531462233582, 11.1136011781754, 3.17531462233582, -4.76297193350373, > 11.1136011781754, -4.76297193350373, 3.17531462233582, -4.76297193350373, > -4.76297193350373, -4.76297193350373, 3.17531462233582, 11.1136011781754, > -4.76297193350373, 3.17531462233582, -4.76297193350373, -4.76297193350373, > 11.1136011781754, -3.70453372605846, 4.23375282978109, 4.23375282978109, > 4.23375282978109, -3.70453372605846, -3.70453372605846, -3.70453372605846, > 12.1720393856206, -3.70453372605846, 12.1720393856206, -3.70453372605846, > -3.70453372605846, -3.70453372605846, 12.1720393856206, -3.70453372605846, > -3.70453372605846, 12.1720393856206, -3.70453372605846, 4.23375282978109, > -3.70453372605846, -3.70453372605846, -3.70453372605846, -3.70453372605846, > 4.23375282978109, -3.70453372605846, -3.70453372605846, 4.23375282978109, > -3.70453372605846, -3.70453372605846, -3.70453372605846, -3.43992417419714, > -3.43992417419714, -3.43992417419714, 4.49836238164241, -3.43992417419714, > 4.49836238164241, -3.43992417419714, -3.43992417419714, 4.49836238164241, > -3.43992417419714, -3.43992417419714, -3.43992417419714, 4.49836238164241, > -3.43992417419714, 4.49836238164241, 4.49836238164241, -3.43992417419714, > 4.49836238164241, -3.43992417419714, 12.436648937482, 4.49836238164241, > -3.43992417419714, -3.43992417419714, 4.49836238164241, -3.43992417419714, > -3.43992417419714, -3.43992417419714, -3.43992417419714, -3.43992417419714, > 12.436648937482, -2.11687641489055, -2.11687641489055, -2.11687641489055, > -2.11687641489055, -2.11687641489055, -2.11687641489055, -2.11687641489055, > 13.7596966967886, -2.11687641489055, 5.821410140949, -2.11687641489055, > -2.11687641489055, -2.11687641489055, 13.7596966967886, -2.11687641489055, > -2.11687641489055, 5.821410140949, -2.11687641489055, 5.821410140949, > -2.11687641489055, -2.11687641489055, -2.11687641489055, -2.11687641489055, > 5.821410140949, -2.11687641489055, -2.11687641489055, -2.11687641489055, > -2.11687641489055, -2.11687641489055, -2.11687641489055, -2.38148596675187, > -2.38148596675187, -2.38148596675187, -2.38148596675187, -2.38148596675187, > -2.38148596675187, -2.38148596675187, 13.4950871449272, -2.38148596675187, > 5.55680058908769, -2.38148596675187, -2.38148596675187, -2.38148596675187, > 13.4950871449272, -2.38148596675187, -2.38148596675187, 5.55680058908769, > -2.38148596675187, 5.55680058908769, -2.38148596675187, -2.38148596675187, > -2.38148596675187, -2.38148596675187, 5.55680058908769, -2.38148596675187, > -2.38148596675187, 5.55680058908769, -2.38148596675187, -2.38148596675187, > -2.38148596675187, 5.02758148536505, -2.9107050704745, -2.9107050704745, > -2.9107050704745, -2.9107050704745, -2.9107050704745, -2.9107050704745, > 12.9658680412046, -2.9107050704745, 5.02758148536505, -2.9107050704745, > -2.9107050704745, -2.9107050704745, 12.9658680412046, -2.9107050704745, > -2.9107050704745, 5.02758148536505, -2.9107050704745, 5.02758148536505, > -2.9107050704745, -2.9107050704745, -2.9107050704745, -2.9107050704745, > 5.02758148536505, 5.02758148536505, -2.9107050704745, -2.9107050704745, > 5.02758148536505, -2.9107050704745, -2.9107050704745, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > 6.61523879653296, -1.32304775930659, -1.32304775930659, 6.61523879653296, > -1.32304775930659, -1.32304775930659, 6.61523879653296, 6.61523879653296, > 6.61523879653296, 3.17531462233582, 3.17531462233582, -4.76297193350373, > -4.76297193350373, -4.76297193350373, -4.76297193350373, -4.76297193350373, > 11.1136011781754, 11.1136011781754, 3.17531462233582, 3.17531462233582, > -4.76297193350373, 3.17531462233582, -4.76297193350373, 3.17531462233582, > -4.76297193350373, -4.76297193350373, 3.17531462233582, -4.76297193350373, > -4.76297193350373, -4.76297193350373, 3.17531462233582, -4.76297193350373, > -4.76297193350373, 3.17531462233582, -4.76297193350373, 11.1136011781754, > 3.17531462233582, 3.17531462233582, 3.17531462233582, -0.793828655583955, > -0.793828655583955, -0.793828655583955, -0.793828655583955, > -0.793828655583955, > -0.793828655583955, -0.793828655583955, -0.793828655583955, > -0.793828655583955, > -0.793828655583955, -0.793828655583955, -0.793828655583955, > -0.793828655583955, > -0.793828655583955, -0.793828655583955, -0.793828655583955, > -0.793828655583955, > -0.793828655583955, -0.793828655583955, -0.793828655583955, > -0.793828655583955, > 7.1444579002556, -0.793828655583955, -0.793828655583955, 7.1444579002556, > -0.793828655583955, -0.793828655583955, -0.793828655583955, > 7.1444579002556, > -0.793828655583955, 11.642820281898, -4.23375282978109, 11.642820281898, > -4.23375282978109, -4.23375282978109, -4.23375282978109, 3.70453372605846, > -4.23375282978109, -4.23375282978109, -4.23375282978109, -4.23375282978109, > -4.23375282978109, 3.70453372605846, -4.23375282978109, 3.70453372605846, > -4.23375282978109, 3.70453372605846, -4.23375282978109, -4.23375282978109, > 3.70453372605846, 3.70453372605846, -4.23375282978109, -4.23375282978109, > -4.23375282978109, 11.642820281898, 3.70453372605846, 3.70453372605846, > 3.70453372605846, 3.70453372605846, -4.23375282978109, -1.05843820744527, > 14.8181349042338, -1.05843820744527, -1.05843820744527, -1.05843820744527, > -1.05843820744527, -1.05843820744527, -1.05843820744527, 6.87984834839428, > 6.87984834839428, -1.05843820744527, -1.05843820744527, -1.05843820744527, > -1.05843820744527, -1.05843820744527, -1.05843820744527, -1.05843820744527, > -1.05843820744527, -1.05843820744527, -1.05843820744527, -1.05843820744527, > -1.05843820744527, -1.05843820744527, -1.05843820744527, -1.05843820744527, > -1.05843820744527, -1.05843820744527, -1.05843820744527, -1.05843820744527, > -1.05843820744527, 4.76297193350373, -3.17531462233582, -3.17531462233582, > -3.17531462233582, -3.17531462233582, -3.17531462233582, -3.17531462233582, > -3.17531462233582, -3.17531462233582, -3.17531462233582, -3.17531462233582, > 4.76297193350373, -3.17531462233582, 4.76297193350373, -3.17531462233582, > 4.76297193350373, -3.17531462233582, -3.17531462233582, -3.17531462233582, > 4.76297193350373, 4.76297193350373, -3.17531462233582, -3.17531462233582, > -3.17531462233582, 12.7012584893433, 4.76297193350373, -3.17531462233582, > 4.76297193350373, 4.76297193350373, 4.76297193350373, 3.17531462233582, > 11.1136011781754, -4.76297193350373, -4.76297193350373, -4.76297193350373, > -4.76297193350373, -4.76297193350373, -4.76297193350373, 3.17531462233582, > 3.17531462233582, -4.76297193350373, 3.17531462233582, -4.76297193350373, > 3.17531462233582, -4.76297193350373, 3.17531462233582, -4.76297193350373, > -4.76297193350373, -4.76297193350373, 3.17531462233582, 3.17531462233582, > -4.76297193350373, 3.17531462233582, -4.76297193350373, 11.1136011781754, > 3.17531462233582, 3.17531462233582, 3.17531462233582, 3.17531462233582, > 3.17531462233582, 6.61523879653296, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, 6.61523879653296, -1.32304775930659, > -1.32304775930659, -1.32304775930659, -1.32304775930659, -1.32304775930659, > -1.32304775930659, -1.32304775930659, 6.61523879653296, 6.61523879653296, > 6.61523879653296, -1.32304775930659, -1.32304775930659, -0.264609551861318, > -0.264609551861318, -0.264609551861318, -0.264609551861318, > -0.264609551861318, > -0.264609551861318, -0.264609551861318, -0.264609551861318, > -0.264609551861318, > -0.264609551861318, -0.264609551861318, -0.264609551861318, > 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"rs3052"))) > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.