[BioC] pint
Raquel Mart’inez Garc’ia
rmartinezg at cnio.es
Thu May 6 10:58:20 CEST 2010
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 electrónico, y ...{{dropped:3}}
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