Hello folks, I'm getting this error when I run duplicate correlation: corfit <- duplicateCorrelation(mat@hx, design, ndups=3, spacing=1) Error in glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace = trace) : Starting values give negative fitted values I saw a previous post on the mailing list where this error occurred because of drastically different values in the input matrix, but I don't have that problem so any help would be greatly appreciated. Here's some extra info: GSM219865 GSM219869 GSM219870 GSM219872 Min. : 2.788 Min. : 2.445 Min. : 3.091 Min. : 2.567 1st Qu.: 4.491 1st Qu.: 4.639 1st Qu.: 4.434 1st Qu.: 4.782 Median : 5.252 Median : 5.305 Median : 4.945 Median : 5.450 Mean : 6.051 Mean : 6.030 Mean : 6.045 Mean : 6.032 3rd Qu.: 7.064 3rd Qu.: 6.817 3rd Qu.: 7.231 3rd Qu.: 6.612 Max. :13.602 Max. :14.033 Max. :13.113 Max. :14.167 GSM219879 GSM219880 GSM219881 GSM219882 Min. : 3.201 Min. : 2.832 Min. : 3.058 Min. : 3.144 1st Qu.: 4.512 1st Qu.: 4.530 1st Qu.: 4.490 1st Qu.: 4.531 Median : 5.095 Median : 5.049 Median : 5.124 Median : 5.029 Mean : 6.023 Mean : 6.028 Mean : 6.011 Mean : 6.052 3rd Qu.: 6.886 3rd Qu.: 6.897 3rd Qu.: 7.087 3rd Qu.: 7.087 Max. :13.979 Max. :13.766 Max. :13.600 Max. :13.382 GSM219886 GSM219887 GSM219892 GSM219894 Min. : 3.236 Min. : 3.007 Min. : 3.048 Min. : 2.707 1st Qu.: 4.419 1st Qu.: 4.520 1st Qu.: 4.407 1st Qu.: 4.674 Median : 4.971 Median : 5.146 Median : 4.968 Median : 5.290 Mean : 6.048 Mean : 6.061 Mean : 6.069 Mean : 6.013 3rd Qu.: 7.036 3rd Qu.: 7.023 3rd Qu.: 7.237 3rd Qu.: 6.589 Max. :13.723 Max. :14.208 Max. :13.281 Max. :14.199 GSM219896 GSM219899 GSM219900 GSM219902 Min. : 3.137 Min. : 3.217 Min. : 2.896 Min. : 2.986 1st Qu.: 4.523 1st Qu.: 4.559 1st Qu.: 4.430 1st Qu.: 4.514 Median : 4.960 Median : 5.163 Median : 5.074 Median : 5.090 Mean : 6.046 Mean : 6.026 Mean : 6.035 Mean : 6.002 3rd Qu.: 7.117 3rd Qu.: 6.746 3rd Qu.: 7.074 3rd Qu.: 7.077 Max. :13.824 Max. :13.816 Max. :13.760 Max. :13.700 GSM219903 GSM219905 GSM219907 GSM219909 Min. : 3.014 Min. : 3.179 Min. : 3.062 Min. : 2.756 1st Qu.: 4.465 1st Qu.: 4.418 1st Qu.: 4.372 1st Qu.: 4.693 Median : 5.027 Median : 4.998 Median : 4.885 Median : 5.386 Mean : 6.057 Mean : 6.045 Mean : 6.056 Mean : 6.027 3rd Qu.: 7.280 3rd Qu.: 7.160 3rd Qu.: 7.175 3rd Qu.: 6.380 Max. :13.592 Max. :13.572 Max. :13.637 Max. :14.457 GSM219911 GSM219912 GSM219913 GSM219918 Min. : 3.048 Min. : 1.977 Min. : 2.819 Min. : 2.929 1st Qu.: 4.431 1st Qu.: 4.730 1st Qu.: 4.440 1st Qu.: 4.614 Median : 4.857 Median : 5.303 Median : 4.956 Median : 5.192 Mean : 6.017 Mean : 6.013 Mean : 6.062 Mean : 6.041 3rd Qu.: 7.233 3rd Qu.: 6.513 3rd Qu.: 7.362 3rd Qu.: 6.948 Max. :13.312 Max. :14.396 Max. :13.212 Max. :14.050 GSM219919 GSM219920 GSM219934 GSM219937 Min. : 3.227 Min. : 3.294 Min. : 2.737 Min. : 2.600 1st Qu.: 4.363 1st Qu.: 4.385 1st Qu.: 4.518 1st Qu.: 4.665 Median : 4.991 Median : 4.869 Median : 5.110 Median : 5.318 Mean : 6.059 Mean : 6.041 Mean : 6.039 Mean : 6.030 3rd Qu.: 7.171 3rd Qu.: 7.175 3rd Qu.: 6.915 3rd Qu.: 6.814 Max. :13.454 Max. :13.221 Max. :13.875 Max. :14.067 GSM219938 GSM219939 GSM219940 GSM219943 Min. : 2.946 Min. : 2.861 Min. : 3.266 Min. : 2.729 1st Qu.: 4.676 1st Qu.: 4.635 1st Qu.: 4.362 1st Qu.: 4.584 Median : 5.354 Median : 5.226 Median : 5.048 Median : 5.123 Mean : 6.047 Mean : 6.034 Mean : 6.046 Mean : 6.019 3rd Qu.: 6.909 3rd Qu.: 6.754 3rd Qu.: 7.249 3rd Qu.: 6.928 Max. :14.083 Max. :14.110 Max. :13.329 Max. :13.836 GSM219944 GSM219945 GSM219948 GSM219950 Min. : 2.724 Min. : 3.149 Min. : 2.902 Min. : 2.900 1st Qu.: 4.590 1st Qu.: 4.412 1st Qu.: 4.593 1st Qu.: 4.321 Median : 5.289 Median : 5.076 Median : 5.172 Median : 5.114 Mean : 6.055 Mean : 6.078 Mean : 6.062 Mean : 6.050 3rd Qu.: 6.927 3rd Qu.: 7.097 3rd Qu.: 6.843 3rd Qu.: 7.100 Max. :14.071 Max. :13.596 Max. :13.920 Max. :13.692 GSM219952 GSM219953 GSM219954 GSM219955 Min. : 2.986 Min. : 2.784 Min. : 2.437 Min. : 3.065 1st Qu.: 4.581 1st Qu.: 4.613 1st Qu.: 4.710 1st Qu.: 4.410 Median : 5.221 Median : 5.179 Median : 5.293 Median : 5.094 Mean : 6.043 Mean : 6.042 Mean : 6.048 Mean : 6.050 3rd Qu.: 6.843 3rd Qu.: 6.738 3rd Qu.: 6.552 3rd Qu.: 7.190 Max. :14.131 Max. :13.695 Max. :14.046 Max. :13.209 GSM219958 GSM219965 GSM219970 GSM219975 Min. : 2.868 Min. : 3.196 Min. : 2.765 Min. : 3.061 1st Qu.: 4.501 1st Qu.: 4.417 1st Qu.: 4.426 1st Qu.: 4.662 Median : 5.162 Median : 4.932 Median : 5.103 Median : 5.303 Mean : 6.070 Mean : 6.044 Mean : 6.028 Mean : 6.039 3rd Qu.: 7.001 3rd Qu.: 7.196 3rd Qu.: 6.940 3rd Qu.: 6.500 Max. :13.765 Max. :13.310 Max. :13.648 Max. :14.177 GSM219976 GSM219977 GSM219978 GSM219980 Min. : 3.393 Min. : 3.170 Min. : 2.694 Min. : 2.999 1st Qu.: 4.375 1st Qu.: 4.373 1st Qu.: 4.636 1st Qu.: 4.711 Median : 4.894 Median : 5.021 Median : 5.185 Median : 5.316 Mean : 6.030 Mean : 6.064 Mean : 6.035 Mean : 6.013 3rd Qu.: 7.049 3rd Qu.: 7.179 3rd Qu.: 6.589 3rd Qu.: 6.377 Max. :13.042 Max. :13.413 Max. :13.906 Max. :13.930 GSM219981 Min. : 3.035 1st Qu.: 4.419 Median : 4.998 Mean : 6.064 3rd Qu.: 7.091 Max. :13.186 > dim(mat@hx) [1] 1077 49 > mat@hx[1:6,] GSM219865 GSM219869 GSM219870 GSM219872 GSM219879 GSM219880 GSM219881 MIRNA174 8.881515 13.19956 12.29140 13.38759 13.13721 12.91034 12.76761 MIRNA174 8.881515 13.19956 12.29140 13.38759 13.13721 12.91034 12.76761 MIRNA174 8.881515 13.19956 12.29140 13.38759 13.13721 12.91034 12.76761 MIRNA175 10.424014 13.95789 13.07468 14.16651 13.93700 13.75428 13.59964 MIRNA175 10.424014 13.95789 13.07468 14.16651 13.93700 13.75428 13.59964 MIRNA175 10.424014 13.95789 13.07468 14.16651 13.93700 13.75428 13.59964 GSM219882 GSM219886 GSM219887 GSM219892 GSM219894 GSM219896 GSM219899 MIRNA174 12.56916 12.82551 13.16155 12.43174 13.33032 12.83228 12.93335 MIRNA174 12.56916 12.82551 13.16155 12.43174 13.33032 12.83228 12.93335 MIRNA174 12.56916 12.82551 13.16155 12.43174 13.33032 12.83228 12.93335 MIRNA175 13.37011 13.68271 13.96500 13.28058 14.19234 13.69705 13.76962 MIRNA175 13.37011 13.68271 13.96500 13.28058 14.19234 13.69705 13.76962 MIRNA175 13.37011 13.68271 13.96500 13.28058 14.19234 13.69705 13.76962 GSM219900 GSM219902 GSM219903 GSM219905 GSM219907 GSM219909 GSM219911 MIRNA174 12.93294 12.84814 12.78597 12.79087 12.68306 13.49380 12.35723 MIRNA174 12.93294 12.84814 12.78597 12.79087 12.68306 13.49380 12.35723 MIRNA174 12.93294 12.84814 12.78597 12.79087 12.68306 13.49380 12.35723 MIRNA175 13.70059 13.64676 13.57370 13.57222 13.52558 14.36265 13.23234 MIRNA175 13.70059 13.64676 13.57370 13.57222 13.52558 14.36265 13.23234 MIRNA175 13.70059 13.64676 13.57370 13.57222 13.52558 14.36265 13.23234 GSM219912 GSM219913 GSM219918 GSM219919 GSM219920 GSM219934 GSM219937 MIRNA174 13.53402 12.27678 13.15308 12.54759 12.38596 12.78409 12.35020 MIRNA174 13.53402 12.27678 13.15308 12.54759 12.38596 12.78409 12.35020 MIRNA174 13.53402 12.27678 13.15308 12.54759 12.38596 12.78409 12.35020 MIRNA175 14.39575 13.15638 13.87750 13.37227 13.13537 13.67619 13.36468 MIRNA175 14.39575 13.15638 13.87750 13.37227 13.13537 13.67619 13.36468 MIRNA175 14.39575 13.15638 13.87750 13.37227 13.13537 13.67619 13.36468 GSM219938 GSM219939 GSM219940 GSM219943 GSM219944 GSM219945 GSM219948 MIRNA174 12.69961 13.04254 12.40181 12.94058 13.15582 12.61323 12.98207 MIRNA174 12.69961 13.04254 12.40181 12.94058 13.15582 12.61323 12.98207 MIRNA174 12.69961 13.04254 12.40181 12.94058 13.15582 12.61323 12.98207 MIRNA175 13.64537 13.85869 13.28368 13.73350 13.98935 13.48931 13.80361 MIRNA175 13.64537 13.85869 13.28368 13.73350 13.98935 13.48931 13.80361 MIRNA175 13.64537 13.85869 13.28368 13.73350 13.98935 13.48931 13.80361 GSM219950 GSM219952 GSM219953 GSM219954 GSM219955 GSM219958 GSM219965 MIRNA174 12.81962 13.27037 12.72672 13.10274 12.32595 12.87308 12.32967 MIRNA174 12.81962 13.27037 12.72672 13.10274 12.32595 12.87308 12.32967 MIRNA174 12.81962 13.27037 12.72672 13.10274 12.32595 12.87308 12.32967 MIRNA175 13.68518 14.06946 13.63226 13.91247 13.19594 13.66014 13.18479 MIRNA175 13.68518 14.06946 13.63226 13.91247 13.19594 13.66014 13.18479 MIRNA175 13.68518 14.06946 13.63226 13.91247 13.19594 13.66014 13.18479 GSM219970 GSM219975 GSM219976 GSM219977 GSM219978 GSM219980 GSM219981 MIRNA174 12.66376 13.28257 12.04305 12.46820 13.02737 13.00563 12.22126 MIRNA174 12.66376 13.28257 12.04305 12.46820 13.02737 13.00563 12.22126 MIRNA174 12.66376 13.28257 12.04305 12.46820 13.02737 13.00563 12.22126 MIRNA175 13.56579 14.06224 12.95079 13.27818 13.82855 13.78838 13.02881 MIRNA175 13.56579 14.06224 12.95079 13.27818 13.82855 13.78838 13.02881 MIRNA175 13.56579 14.06224 12.95079 13.27818 13.82855 13.78838 13.02881 > sessionInfo() R version 2.9.1 (2009-06-26) i486-pc-linux-gnu locale: LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_IE .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] statmod_1.4.0 limma_2.18.2 vsn_3.12.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affy_1.22.0 affyio_1.12.0 grid_2.9.1 [4] lattice_0.17-25 preprocessCore_1.6.0 -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland [[alternative HTML version deleted]]