[BioC] rbind of MALists

Matthew Scholz schmatthew at gmail.com
Wed Jun 14 16:54:55 CEST 2006


Gordon,

Thank you for your advice. I'm still having a problem rbinding my
MALists and have attached below the output of the commands you asked
me to execute. While you are correct that I missed a "$'" in my
genesStatus syntax, correcting this does not seem to remedy the
problem. In addition, I realized that whether I correct this or not I
have no problem doing:

new = rbind(RGAmodel, RGAmodel)

but cannot do:

new = rbind(RGAmodel, RGBmodel)

Dawn slowly broke over my cratered skull when I noticed that the
column names for these two lists are not the same. I wanted to test
whether this was the problem, but noticed that when I tried:

colnames(RGBmodel) = colnames(RGAmodel)

Error in "colnames<-"(`*tmp*`, value = c("11_1.7A.003_133",
"11_1.7A.004_134",  :
        'dimnames' applied to non-array

According to the help for dimnames.MAList, colnames is supposed to
work 'as expected', so I'm not sure what the hang up is.

If it helps, here is the output from the commands you asked me to execute:

> show(RGAmodel)
An object of class "MAList"
$weights
     11_1.7A.003_133 11_1.7A.004_134 11_1.7A.005_135 11_1.7A.006_136
[1,]               1               0               1               1
[2,]               1               1               1               0
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.007_137 11_1.7A.008_138 11_1.7A.009_139 11_1.7A.010_140
[1,]               1               1               1               1
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.011_141 11_1.7A.012_142 11_1.7A.013_143 11_1.7A.014_144
[1,]               0               1               1               0
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.015_145 11_1.7A.016_146 11_1.7A.017_147 11_1.7A.018_148
[1,]               1               1               1               0
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.019_149 11_1.7A.020_150 11_1.7A.021_151 11_1.7A.022_152
[1,]               1               1               1               1
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.023_153 11_1.7A.024_154 11_1.7A.025_155 11_1.7A.026_156
[1,]               1               1               1               0
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.027_157 11_1.7A.028_158 11_1.7A.029_159 11_1.7A.030_160
[1,]               1               1               1               1
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
     11_1.7A.031_161 11_1.7A.032_162 11_1.7A.033_163 11_1.7A.034_164
[1,]               1               1               1               1
[2,]               1               1               1               1
[3,]               1               1               1               1
[4,]               1               1               1               1
[5,]               1               1               1               1
32443 more rows ...

$targets
[1] "11_1.7A.003_133.gpr" "11_1.7A.004_134.gpr" "11_1.7A.005_135.gpr"
[4] "11_1.7A.006_136.gpr" "11_1.7A.007_137.gpr"
27 more rows ...

$genes
  Block Row Column         ID
1     1   1      1 MZ00040724
2     1   1      2 MZ00040730
3     1   1      3 MZ00040748
4     1   1      4 MZ00040754
5     1   1      5 MZ00040772
32443 more rows ...

$source
[1] "genepix"

$printer
$ngrid.r
[1] 12

$ngrid.c
[1] 4

$nspot.r
[1] 26

$nspot.c
[1] 26

$ndups
[1] 1

$spacing
[1] 1

attr(,"class")
[1] "PrintLayout"

$genesStatus
[1] "oligo" "oligo" "oligo" "oligo" "oligo"
32443 more elements ...

$M
     11_1.7A.003_133 11_1.7A.004_134 11_1.7A.005_135 11_1.7A.006_136
[1,]      -1.1025283      -0.4665859      -1.2443265      -0.7460295
[2,]      -0.6452398       1.1784430      -1.1102468      -0.2550268
[3,]       0.1586242       0.1141068      -0.3987019      -0.7830444
[4,]       0.9701582      -1.1933750       0.2630213      -0.1432319
[5,]      -0.5505187       1.2380281      -0.8449859       0.5921425
     11_1.7A.007_137 11_1.7A.008_138 11_1.7A.009_139 11_1.7A.010_140
[1,]      0.30430951      -0.7297204      -0.1255653       1.5487331
[2,]     -0.29503663       0.7602903      -0.3451359      -0.3052871
[3,]     -0.23589470      -0.4166166      -0.1707812       0.7727964
[4,]     -0.65639565      -1.0222411      -0.3986391       1.7082251
[5,]     -0.09215817       0.6226440       0.0880441      -0.6095265
     11_1.7A.011_141 11_1.7A.012_142 11_1.7A.013_143 11_1.7A.014_144
[1,]      -1.6717252     0.355848103     -1.29343084      -0.8880984
[2,]      -0.1466151     0.009279503     -0.02537785      -0.1948173
[3,]      -0.2785056     0.455366117     -0.37567263      -0.3661568
[4,]       0.2075807    -0.542606661      0.09641300      -0.4351683
[5,]      -0.6158258     1.054632489     -0.47918786      -0.5904125
     11_1.7A.015_145 11_1.7A.016_146 11_1.7A.017_147 11_1.7A.018_148
[1,]       0.7297666      -0.2570969      -0.8220234      -1.1114843
[2,]      -0.3067739      -1.0323099       0.1110739      -0.3244558
[3,]      -0.9335876      -0.8589877       0.5613253       1.2955507
[4,]      -1.8261876      -0.6935107       1.1364680       0.3303186
[5,]      -0.4911613       0.5464649      -1.9364591       2.0930105
     11_1.7A.019_149 11_1.7A.020_150 11_1.7A.021_151 11_1.7A.022_152
[1,]       2.3664853       1.3320860      -0.3395910      -1.0286536
[2,]      -0.6584151      -0.7052792      -0.2159054       0.3553915
[3,]       0.8548703       0.8395172       0.5626271       0.4381228
[4,]      -0.2767574      -0.8201371       0.9660881       0.9853922
[5,]      -0.1787140       0.4437432      -0.6651411      -0.3365878
     11_1.7A.023_153 11_1.7A.024_154 11_1.7A.025_155 11_1.7A.026_156
[1,]     -1.62025658      -1.6703972      -1.5040131     -1.59465519
[2,]     -1.03440276      -0.2526851       0.1587630      0.11541673
[3,]     -0.09198932      -0.2073343       0.5093910      0.52420791
[4,]      0.48629916      -1.0061265      -0.1088980     -0.04149065
[5,]      0.03810017      -0.4870690       0.1284282      1.72733520
     11_1.7A.027_157 11_1.7A.028_158 11_1.7A.029_159 11_1.7A.030_160
[1,]      -1.2125924      -2.0282105      -1.6003112      -1.9826522
[2,]      -0.9812115       0.8340283      -1.0061678      -0.1848412
[3,]      -0.1897043      -0.6798321      -0.4078205      -0.9279219
[4,]       0.2455694      -0.9094738       0.9320699      -0.3152323
[5,]      -0.1796293       0.8590802      -1.2228430      -1.1046028
     11_1.7A.031_161 11_1.7A.032_162 11_1.7A.033_163 11_1.7A.034_164
[1,]      0.45430037      -1.7238789      0.01628412       1.7308700
[2,]      0.34254820       0.7655072     -0.07430473       0.1912626
[3,]      0.08683668      -2.0641031     -0.97659228       0.2502367
[4,]     -0.17631164      -0.4071476     -1.51322855       0.8134877
[5,]      0.50517021      -1.8551115      0.31450027       1.1886982
32443 more rows ...

$A
     11_1.7A.003_133 11_1.7A.004_134 11_1.7A.005_135 11_1.7A.006_136
[1,]        7.067742        6.314364        7.187490        8.572728
[2,]        9.012202       10.321708       11.347639        9.619762
[3,]        8.820257        9.480137       11.152441       10.103530
[4,]        9.113281        8.818256        9.237627        8.845255
[5,]       11.305631       11.811662       12.468975       11.767829
     11_1.7A.007_137 11_1.7A.008_138 11_1.7A.009_139 11_1.7A.010_140
[1,]       13.216188       12.753544       11.138413       11.665765
[2,]       10.100641        9.813759       10.956860       10.238678
[3,]       10.869273       10.015065       10.561280       10.431992
[4,]        9.805024        8.536809        8.462371        8.964282
[5,]       11.478938       11.761713       13.455756       12.570729
     11_1.7A.011_141 11_1.7A.012_142 11_1.7A.013_143 11_1.7A.014_144
[1,]        6.721641        5.932721        6.953904        6.500138
[2,]       11.400485       11.968232       11.727238       10.978747
[3,]       10.459052       10.645864       10.611947       10.003722
[4,]        9.042731        9.411245        8.887326        8.597725
[5,]       12.874397       13.502570       13.623161       12.659994
     11_1.7A.015_145 11_1.7A.016_146 11_1.7A.017_147 11_1.7A.018_148
[1,]        5.033375        5.723043        6.116828        6.842104
[2,]       10.362262        9.771524        9.590353       11.194014
[3,]        9.913907        8.376788        7.768291        9.634776
[4,]        8.512061        7.199640        8.130019        9.597877
[5,]       12.092490       11.085349       10.279450       12.161460
     11_1.7A.019_149 11_1.7A.020_150 11_1.7A.021_151 11_1.7A.022_152
[1,]       11.995929       13.127644        9.225215        10.92839
[2,]        9.592951        9.717794       10.451920        11.36524
[3,]        9.560552        9.686789       10.551277        10.45670
[4,]        8.812669        9.390420        8.927714         8.96156
[5,]       11.777360       11.345326       12.712251        13.00112
     11_1.7A.023_153 11_1.7A.024_154 11_1.7A.025_155 11_1.7A.026_156
[1,]        7.080557        6.774674        6.905477        6.894019
[2,]       11.728278       11.298933       10.281641       11.074350
[3,]       10.743400        9.924770        8.743135        9.325957
[4,]        9.496900        8.646215        7.675072        8.711542
[5,]       13.572918       12.252402       12.518318       11.763458
     11_1.7A.027_157 11_1.7A.028_158 11_1.7A.029_159 11_1.7A.030_160
[1,]        6.948659        6.849376        7.018617        7.895815
[2,]       10.500807       10.238772       10.185412       11.475047
[3,]        9.345473        9.949614       10.048936       10.199916
[4,]        8.389225        8.615887        8.910566        9.024467
[5,]       12.117364       12.060297       12.591901       13.183420
     11_1.7A.031_161 11_1.7A.032_162 11_1.7A.033_163 11_1.7A.034_164
[1,]        8.065446       12.870417       13.320382        9.838204
[2,]       11.405467       10.001051        9.212157       10.999377
[3,]       10.927000        9.657809        9.245457        9.777995
[4,]        9.782490        9.239337        8.100707        7.909291
[5,]       13.772576       11.057297       10.929249       12.417927
32443 more rows ...

>  show(RGBmodel)
An object of class "MAList"
$weights
     11_1.7B.003 11_1.7B.004 11_1.7B.005 11_1.7B.006 11_1.7B.007 11_1.7B.008
[1,]           1           1           0           1           1           1
[2,]           1           1           1           1           1           1
[3,]           1           1           1           1           1           1
[4,]           1           1           1           1           1           0
[5,]           1           1           1           1           1           0
     11_1.7B.009 11_1.7B.010 11_1.7B.011 11_1.7B.012 11_1.7B.013 11_1.7B.014
[1,]           1           1           1           1           1           1
[2,]           1           1           0           1           1           0
[3,]           1           0           0           0           1           1
[4,]           0           1           1           1           0           0
[5,]           0           1           1           1           1           1
     11_1.7B.015 11_1.7B.016 11_1.7B.017 11_1.7B.018 11_1.7B.019 11_1.7B.020
[1,]           1           1           1           1           1           1
[2,]           1           1           0           1           1           1
[3,]           1           1           1           1           1           1
[4,]           1           1           0           1           1           1
[5,]           1           1           0           1           1           1
     11_1.7B.021 11_1.7B.022 11_1.7B.023 11_1.7B.024 11_1.7B.025 11_1.7B.026
[1,]           1           0           1           1           1           1
[2,]           1           0           1           1           1           1
[3,]           1           1           1           1           1           1
[4,]           0           0           1           0           1           1
[5,]           1           1           1           1           1           1
     11_1.7B.027 11_1.7B.028 11_1.7B.029 11_1.7B.030 11_1.7B.031 11_1.7B.032
[1,]           1           0           1           1           0           1
[2,]           0           1           1           1           1           1
[3,]           1           0           0           1           0           1
[4,]           0           0           1           1           1           1
[5,]           1           1           1           1           1           1
     11_1.7B.033 11_1.7B.034
[1,]           1           1
[2,]           1           1
[3,]           1           1
[4,]           1           1
[5,]           0           1
32443 more rows ...

$targets
[1] "11_1.7B.003.gpr" "11_1.7B.004.gpr" "11_1.7B.005.gpr" "11_1.7B.006.gpr"
[5] "11_1.7B.007.gpr"
27 more rows ...

$genes
  Block Row Column         ID        Name
1     1   1      1 MZ00002380  AZM4_14521
2     1   1      2 MZ00002386  AZM4_49988
3     1   1      3 MZ00002404 AZM4_100937
4     1   1      4 MZ00002410 AZM4_135577
5     1   1      5 MZ00002428  AZM4_79828
32443 more rows ...

$source
[1] "genepix"

$printer
$ngrid.r
[1] 12

$ngrid.c
[1] 4

$nspot.r
[1] 26

$nspot.c
[1] 26

$ndups
[1] 1

$spacing
[1] 1

attr(,"class")
[1] "PrintLayout"

$genesStatus
[1] "oligo" "oligo" "oligo" "oligo" "oligo"
32443 more elements ...

$M
     11_1.7B.003 11_1.7B.004 11_1.7B.005 11_1.7B.006 11_1.7B.007 11_1.7B.008
[1,]  1.19167753  0.56248514  0.53057343  -0.2368892  0.08951696  0.02770597
[2,]  0.40105375 -0.17197218  0.04136003   0.1987125 -0.61484562  0.49959770
[3,] -0.04242721 -0.08305925  0.41395437   0.4196492 -0.23034644 -0.28972366
[4,] -1.42987096 -1.13447249 -0.92317619  -0.8872826 -0.70401948 -0.76497663
[5,]  1.30575510 -0.70657723 -0.43743378  -0.7544761  0.40971434  0.78362609
     11_1.7B.009 11_1.7B.010 11_1.7B.011 11_1.7B.012 11_1.7B.013 11_1.7B.014
[1,]   0.3479275 -0.36757062 -0.02604215  -0.2367116  0.33686435 -0.74121990
[2,]  -0.2402348  0.01589095  0.01272487  -1.1285366  0.36399265 -0.19820755
[3,]  -0.6470032  1.14420768  0.97352742  -0.8948713  0.10062537 -0.57570915
[4,]  -0.8760413 -0.22059179 -1.34896806  -1.2611718 -0.06204539  0.06817653
[5,]   0.2033776  0.31256786 -1.23194515   1.6987695 -1.71248001  1.30498581
      11_1.7B.015 11_1.7B.016 11_1.7B.017 11_1.7B.018 11_1.7B.019 11_1.7B.020
[1,]  0.495959729  -0.1746219   0.1797239   0.7036316 -0.16213818   0.4067894
[2,] -0.003739179   0.2453268  -0.1621772   2.3024631 -0.07363043   0.7304520
[3,]  0.159801229  -0.4700611  -0.9515640  -0.4111921 -1.18104994  -1.2124029
[4,]  0.114155727  -0.3548972   0.2433237  -0.9400939 -1.42271526  -2.3694402
[5,]  0.544882076  -0.1736855   0.3748293  -0.5401609 -1.54493748  -2.1387979
     11_1.7B.021 11_1.7B.022 11_1.7B.023 11_1.7B.024 11_1.7B.025 11_1.7B.026
[1,]  0.87601557  0.01696255   1.5156342  -0.1698067   0.2883991  -0.2841663
[2,]  1.13356017  0.66054567   1.7647670  -0.2842037  -0.7659591  -1.1996018
[3,] -0.50232181  0.27405068  -0.1089857  -0.2146920  -1.0162737  -0.9083534
[4,] -0.01466337 -0.34657287  -1.9505463   0.4416073  -1.4860429  -0.5330481
[5,]  2.27579475  2.72701260  -1.3792235   0.6699561   0.1794446  -0.4531982
     11_1.7B.027 11_1.7B.028 11_1.7B.029 11_1.7B.030 11_1.7B.031 11_1.7B.032
[1,]   0.2316674  -1.6718436  -2.5984281  0.09607997  -0.4244763   1.7807719
[2,]   0.7481809  -0.1658066   0.6723337 -0.57179068  -0.9190142   0.7851527
[3,]   0.4386763  -0.5111595  -0.6678957 -0.85591202  -0.7804590  -0.8124523
[4,]   0.3238812  -1.2772746  -0.6445291 -1.46969652  -1.3270658  -1.7383684
[5,]   1.4530629  -0.6506754   1.1897330 -2.02066054  -0.0973254   0.4464960
     11_1.7B.033 11_1.7B.034
[1,]  0.10719492   1.1977097
[2,]  0.68606341   0.6504811
[3,]  0.08184476  -0.4843391
[4,] -0.71939913  -1.6988968
[5,]  0.04671642  -0.5900561
32443 more rows ...

$A
     11_1.7B.003 11_1.7B.004 11_1.7B.005 11_1.7B.006 11_1.7B.007 11_1.7B.008
[1,]    5.867874    5.795048    6.606571    5.203723    4.594767    5.611233
[2,]    6.077780    5.856446    6.165828    5.207372    4.983079    6.273711
[3,]    6.864595    6.964256    6.980932    5.510978    4.754364    5.671809
[4,]    6.116169    6.978315    6.171485    5.522281    5.728463    6.463469
[5,]   10.855069   11.316873   11.023288    9.124135    5.120124    5.851479
     11_1.7B.009 11_1.7B.010 11_1.7B.011 11_1.7B.012 11_1.7B.013 11_1.7B.014
[1,]    5.730457    5.481935    4.769377    6.083786    5.007966    5.141382
[2,]    5.865751    8.588466    6.760794    7.065903    5.453762    6.706594
[3,]    5.710088    6.986815    6.362918    7.595231    5.448007    5.637921
[4,]    6.230352    6.397243    6.516190    7.086991    6.891454    6.854516
[5,]    6.227262    7.091886    8.738373   10.351816    9.945595    9.146608
     11_1.7B.015 11_1.7B.016 11_1.7B.017 11_1.7B.018 11_1.7B.019 11_1.7B.020
[1,]    4.466604    5.249380    5.773108    4.728652    5.411685    3.853863
[2,]    4.929356    5.741409    6.388231    8.304058    5.217227    3.680880
[3,]    5.051200    6.007722    5.661640    6.647807    4.981389    4.680015
[4,]    4.650070    6.526112    6.767180    5.274246    5.715423    4.620214
[5,]    5.397292    6.021343    6.059574    6.737000    7.510173   10.783081
     11_1.7B.021 11_1.7B.022 11_1.7B.023 11_1.7B.024 11_1.7B.025 11_1.7B.026
[1,]    7.050508    6.661605    6.715157    5.441985    4.906303    4.089464
[2,]    5.395864    6.549262    8.524508    5.449342    5.076816    5.204264
[3,]    6.318431    6.720648    5.547102    5.422083    5.247963    4.705592
[4,]    7.760107    6.975563    4.656751    6.334097    6.063947    5.693239
[5,]    8.760490   10.588693    7.961084    6.459167   10.086370    7.462502
     11_1.7B.027 11_1.7B.028 11_1.7B.029 11_1.7B.030 11_1.7B.031 11_1.7B.032
[1,]    5.456981    6.002540    6.858067    5.221205    6.810400    5.971652
[2,]    6.286845    6.897648    5.487945    5.378415    9.072984    5.824060
[3,]    5.908124    6.712162    6.534923    5.714359    6.715101    5.066708
[4,]    6.463484    6.641324    5.985717    5.886168    6.048547    5.435426
[5,]    8.315183    9.846694   11.351338    9.069206    7.598162    6.237865
     11_1.7B.033 11_1.7B.034
[1,]    5.203755    4.379203
[2,]    6.236316    4.191219
[3,]    5.174114    4.214278
[4,]    5.934155    5.716151
[5,]    6.986043    5.391660
32443 more rows ...

Thanks again for you sage advice,

Matt


On 6/13/06, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
> > Date: Mon, 12 Jun 2006 15:20:24 -0700
> > From: "Matthew Scholz" <schmatthew at gmail.com>
> > Subject: [BioC] rbind of MALists
> > To: bioconductor at stat.math.ethz.ch
> >
> > Hi all,
> >
> > I'm trying to combine two MALists, named RGAmodel and RGBmodel, using
> > rbind and am running into the following problem:
> >
> >> rbind(RGAmodel, RGBmodel)
> > Error in match.names(clabs, names(xi)) : names don't match previous names:
> >         Name
> > In addition: Warning message:
> > longer object length
> >         is not a multiple of shorter object length in: clabs == nmi
> >
> > I checked that the names were the same for each object and that the
> > classes and dimensions match:
> >
> >> names(RGAmodel)
> > [1] "weights"     "targets"     "genes"       "source"      "printer"
> > [6] "genesStatus" "M"           "A"
> >> names(RGBmodel)
> > [1] "weights"     "targets"     "genes"       "source"      "printer"
> > [6] "genesStatus" "M"           "A"
> >
> >> class(RGAmodel)
> > [1] "MAList"
> > attr(,"package")
> > [1] "limma"
> >
> >> class(RGBmodel)
> > [1] "MAList"
> > attr(,"package")
> > [1] "limma"
> >
> >> dim(RGAmodel)
> > [1] 32448    32
> >
> >> dim(RGBmodel)
> > [1] 32448    32
> >
> > What am I doing wrong? I'm using R2.3.0 and Bioconductor 1.7
> >
> > Thanks,
> >
> > Matt
> >
> > --
> > Matt Scholz
> > Senior Research Specialist
> > Department of Plant Sciences
> > University of Arizona
> > (520) 621-1695
>
> Dear Matt,
>
> Firstly, your MAList objects contain non-standard components "genesStatus" which are not
> understood by limma, so it will not be possible for rbind() to work correctly on your objects.  Is
> it possible that you meant to follow the limma User's Guide advice on setting the control status
> of each probe (e.g., on page 18)
>
>   RG$genes$Status <- controlStatus(spottypes, RG)
>
> but have missed out the second $-sign?  If you did, that would produce the extra component in the
> data objects that we see above.
>
> You can remove the non-standard components by
>
>    RGAmodel$genesStatus <- NULL
>    RGBmodel$genesStatus <- NULL
>
> Do the objects rbind() correctly after removing these components?  If the problem persists, can
> you please show the output from
>
>   show(RGAmodel)
>   show(RGBmodel)
>
> so we can see more information.
>
> Best wishes
> Gordon
>
>
>


-- 
Matt Scholz
Senior Research Specialist
Department of Plant Sciences
University of Arizona
(520) 621-1695



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