the "%g" indicates a bug somewhere but not relevant to your problem.  i
would suspect that your problem is arising from the existence of perfect
numerical duplicates among the rows of the copy number data.
ENSG00000117620 and ENSG00000156875 seem to have the same values.

On Thu, May 6, 2010 at 4:58 AM, Raquel Mart’inez Garc’ia <rmartinezg@cnio.es
> wrote:

> I've tried using the function pint, but only the two methods (PPCA and PFA)
> have worked.
> Data:
>
> GeneExp$data
>
>                     JH015         421       JH024         374          159
> ENSG00000162688  0.08291135  0.16453909  0.13894691  0.07312734
>  0.138530121
> ENSG00000130939 -0.07490988  0.11453929 -0.14742123 -0.06672798
> -0.061729848
> ENSG00000117620 -0.24785807 -0.30378843 -0.27489672 -0.35237202
> -0.235000347
> ENSG00000156875 -0.18080537 -0.21386545 -0.14961124 -0.23491562
> -0.277538310
> ENSG00000156876 -0.18914190 -0.16328418 -0.20546032 -0.33497900
> -0.255275484
> ENSG00000122435 -0.02141891 -0.02676549 -0.07346127 -0.02799705
> -0.002818914
>                       281         410          420         247       JH011
> ENSG00000162688 -0.01453460  0.15901276  0.037195910  0.04639360
>  0.07765883
> ENSG00000130939 -0.07262894 -0.08138451 -0.002648273 -0.12239380
> -0.15212017
> ENSG00000117620 -0.35659091 -0.35364242 -0.298346298 -0.33229155
>  0.16163296
> ENSG00000156875 -0.25045916 -0.19531454 -0.384359883 -0.19592723
> -0.20968993
> ENSG00000156876 -0.23365840 -0.28810579 -0.379150470 -0.06212257
> -0.19538242
> ENSG00000122435 -0.16349307 -0.20059094 -0.284837478 -0.01789416
> -0.08107138
>                     JH034         JH027       JH033         163        219
> ENSG00000162688 -0.07682540 -6.149562e-05 -0.02263361  0.04281750
> -0.1005669
> ENSG00000130939 -0.09270105 -1.501213e-01 -0.25812785 -0.02275307
> -0.2809320
> ENSG00000117620 -0.07231041  4.172350e-02 -0.30821137 -0.36844042
> -0.1410397
> ENSG00000156875 -0.27982765 -2.115677e-01 -0.29566490 -0.21444092
> -0.2723123
> ENSG00000156876 -0.34434520 -2.015085e-01 -0.18165317 -0.19165777
> -0.2812740
> ENSG00000122435 -0.28201917 -1.617882e-01 -0.09178899 -0.20044987
> -0.3498142
>                       294         253          265          354         A6L
> ENSG00000162688 -0.21161332 -0.03323369  0.094814482  0.089544939
>  0.10519893
> ENSG00000130939 -0.03301957  0.08613782 -0.007763271  0.007429982
> -0.05860285
> ENSG00000117620 -0.42661807 -0.29556335 -0.433183809 -0.381689379
>  0.04769950
> ENSG00000156875 -0.33143537 -0.25553338 -0.284907129 -0.205499694
> -0.17894080
> ENSG00000156876 -0.43304955 -0.29417152 -0.307144670 -0.167636252
> -0.22033642
> ENSG00000122435 -0.29220346 -0.27336087 -0.098205676 -0.022510610
> -0.10057796
>                       291        286          266          215         185
> ENSG00000162688  0.05087102  0.1993795  0.049927944 -0.002866419
> -0.02899360
> ENSG00000130939 -0.26594950 -0.0661677 -0.111860030  0.032596272
> -0.08358910
> ENSG00000117620  0.10130492 -0.2910858  0.004766455 -0.323354334
> -0.44620803
> ENSG00000156875 -0.27403293 -0.1631991 -0.248196629 -0.321544370
> -0.46658865
> ENSG00000156876 -0.30258211 -0.1210534 -0.221077249 -0.271762346
> -0.18614635
> ENSG00000122435 -0.22892602 -0.1567120 -0.099516089 -0.325825205
>  0.02515607
>                       287         140        194         198      JH010
> ENSG00000162688  0.05311155  0.04407312  0.0341894  0.09354113  0.1269307
> ENSG00000130939 -0.14374302 -0.01845360 -0.0989010 -0.03487187 -0.1032288
> ENSG00000117620  0.10084557 -0.18926795  0.1618709 -0.37706661 -0.3456850
> ENSG00000156875 -0.17277866 -0.23577380 -0.1284404 -0.19361255 -0.2911650
> ENSG00000156876 -0.14192276 -0.28938330 -0.1794656 -0.23567196 -0.2191114
> ENSG00000122435 -0.15398751 -0.13318159 -0.1566271 -0.03520345 -0.1184283
>
>
>
> GeneCopyNumber$data
>
>                    JH015         421        JH024          374          159
> ENSG00000162688 0.01451634  0.01536253 2.242446e-02 0.0004585763
> 4.609309e-02
> ENSG00000130939 0.09518705 -0.01547407 5.385476e-06 0.0006993714
> 2.694937e-07
> ENSG00000117620 0.01451634  0.01536253 2.242446e-02 0.0004585763
> 4.609309e-02
> ENSG00000156875 0.01451634  0.01536253 2.242446e-02 0.0004585763
> 4.609309e-02
> ENSG00000156876 0.01451634  0.01536253 2.242446e-02 0.0004585763
> 4.609309e-02
> ENSG00000122435 0.01451634  0.01536253 2.242446e-02 0.0004585763
> 4.609309e-02
>                       281         410          420          247      JH011
> ENSG00000162688 0.001691496 0.009146616 0.1158556854 -0.029485044
> -0.1636021
> ENSG00000130939 0.010524919 0.081446191 0.0002758042  0.004618593
> -0.3156647
> ENSG00000117620 0.001691496 0.009146616 0.1158556854 -0.029485044
> -0.1636021
> ENSG00000156875 0.001691496 0.009146616 0.1158556854 -0.029485044
> -0.1636021
> ENSG00000156876 0.001691496 0.009146616 0.1158556854 -0.029485044
> -0.1636021
> ENSG00000122435 0.001691496 0.009146616 0.1158556854 -0.029485044
> -0.1636021
>                      JH034        JH027        JH033           163
> ENSG00000162688 3.211448e-07 0.0472749756 4.652529e-08  0.0009843382
> ENSG00000130939 7.241995e-04 0.0001827229 1.732236e-05 -0.0273445131
> ENSG00000117620 3.211448e-07 0.0472749756 4.652529e-08  0.0009843382
> ENSG00000156875 3.211448e-07 0.0472749756 4.652529e-08  0.0009843382
> ENSG00000156876 3.211448e-07 0.0472749756 4.652529e-08  0.0009843382
> ENSG00000122435 3.211448e-07 0.0472749756 4.652529e-08  0.0107513061
>                        219           294           253           265
> ENSG00000162688 2.123433e-17  0.0006444035  9.600902e-08  6.626342e-06
> ENSG00000130939 1.321921e-06 -0.0009132755 -2.376673e-02 -3.709579e-02
> ENSG00000117620 2.123433e-17  0.0006444035  9.600902e-08  6.626342e-06
> ENSG00000156875 2.123433e-17  0.0006444035  9.600902e-08  6.626342e-06
> ENSG00000156876 2.123433e-17  0.0006444035  9.600902e-08  6.626342e-06
> ENSG00000122435 2.123433e-17  0.0006444035  8.808255e-05  6.626342e-06
>                        354          A6L           291           286
> ENSG00000162688  0.004417712  0.000166896  7.839781e-06  1.304294e-05
> ENSG00000130939 -0.047793177 -0.003999653 -1.005482e-03 -2.584692e-01
> ENSG00000117620  0.004417712  0.000166896  7.839781e-06  1.304294e-05
> ENSG00000156875  0.004417712  0.000166896  7.839781e-06  1.304294e-05
> ENSG00000156876  0.004417712  0.000166896  7.839781e-06  1.304294e-05
> ENSG00000122435  0.004417712  0.000166896  7.839781e-06  3.720726e-02
>                        266          215           185           287
> ENSG00000162688 1.080601e-06 1.763052e-06  2.482773e-09  2.192861e-06
> ENSG00000130939 1.225262e-01 4.508532e-02 -1.573191e-02 -8.160346e-02
> ENSG00000117620 1.080601e-06 1.763052e-06  2.482773e-09  2.192861e-06
> ENSG00000156875 1.080601e-06 1.763052e-06  2.482773e-09  2.192861e-06
> ENSG00000156876 1.080601e-06 1.763052e-06  2.482773e-09  2.192861e-06
> ENSG00000122435 9.613601e-04 5.650614e-04  1.475381e-04  2.192861e-06
>                        140          194          198        JH010
> ENSG00000162688 5.390246e-06  0.002723076  0.005339678 8.939409e-06
> ENSG00000130939 5.933826e-04 -0.045733304 -0.014948441 1.989656e-02
> ENSG00000117620 5.390246e-06  0.002723076  0.005339678 8.939409e-06
> ENSG00000156875 5.390246e-06  0.002723076  0.005339678 8.939409e-06
> ENSG00000156876 5.390246e-06  0.002723076  0.005339678 8.939409e-06
> ENSG00000122435 5.390246e-06  0.002723076  0.005339678 1.564054e-02
>
> GeneExp$info   GeneCopyNumber$info
>
>     chr arm loc
> 3920    1   p  20
> 3159    1   p  32
> 6095    1   p  40
> 13213   1   p  51
> 14797   1   p  59
> 10618   1   p  67
>
>
> Error (model <- screen.cgh.mrna
> (geneExp,geneCopyNumber,windowSize=10,chr=1,arm ="p",method="pSimCCA" or
> "pCCA"):
>
> Lapack routine dgesv: system is exactly singular
> or
> system is computationally singular: reciprocal condition number = %g
>
> SessionInfo:
>
> R version 2.11.0 (2010-04-22)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] pint_1.0.0    mvtnorm_0.9-9
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
>
> Can you help me??
>
> --
> ********************************************
>
> Raquel Martinez Garcia, Graduate Student
> Gastrointestinal Cancer Clinical Research Unit
> & Structural Computational Biology Group
> Spanish National Cancer Research Center, CNIO
> Melchor Fernandez Almagro, 3.
> 28029 Madrid, Spain.
> Phone: +34 91 732 80 00 #3015
> rmartinezg@cnio.es
> http://www.cnio.es
>
> ********************************************
>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:3}}
>
>
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