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 at cnio.es http://www.cnio.es ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}

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}} > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hello! Thanks Mr. Carey for your reply. Any genes have the same values because the data are segmented. Now I need to know if the both methods pCCA and pSimCCA have any problems for work with segmented data or do not these methods work for another reason?. Thanks in advance Raquel -- ******************************************** 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 at cnio.es http://www.cnio.es ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}

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