Hi, I noticed a Rdata size issue that's puzzling to me. Attached find 2 example
datasets in text file. Both are 100x5, so the sizes for both text file are the
same. However, when I read them into R, the sizes are much different:
tt<-as.matrix(read.table("tt.txt",header=T,row.names=1))
save(tt,file='tt.RData')
tt.big<-as.matrix(read.table("tt.big.txt",header=T,row.names=1))
save(tt.big,file='tt.big.RData')
"tt.RData" is 2KB while "tt.big.RData" is 5KB. This is not a big deal with the
example datasets, but my real datasets are much larger, the difference is 35MB
vs. 1MB for the RData objects.
The difference between the 2 datasets above is that "tt.big" is a smoothed
version of "tt", so there are a lot less unique values in tt.big than tt, I
guess this is the reason for the difference in sizes of RData objects, can
anyone confirm?
Thanks
John
PC1 PC2 PC3 PC4 PC5
SNP_A-1677174 1.683848 1.975826 2.355682 1.587903
1.157294
SNP_A-1718890 2.061455 1.926552 2.19278 2.071653 2.712994
SNP_A-1678466 2.105124 1.975826 2.128437 1.587903
1.157294
SNP_A-1676440 2.105124 1.975826 2.128437 1.587903
1.157294
SNP_A-1662392 2.105124 1.975826 2.128437 1.587903
1.157294
SNP_A-1685736 2.105124 1.975826 2.128437 1.587903
1.157294
SNP_A-1681384 2.105124 1.975826 2.128437 1.587903
1.157294
SNP_A-1668776 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1642581 1.560647 1.297883 1.458162 1.587903
1.157294
SNP_A-1669029 1.560647 1.297883 1.458162 1.587903
1.157294
SNP_A-1723597 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1718237 1.560647 1.297883 1.458162 1.016043
1.157294
SNP_A-1748467 1.560647 1.297883 1.458162 1.016043
1.157294
SNP_A-1728870 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1669946 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1708099 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1716798 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1701872 2.061455 1.926552 2.19278 1.554699 0.616379
SNP_A-1705537 2.365606 2.652155 2.582983 2.002516
1.023379
SNP_A-1683756 2.365606 2.652155 2.582983 2.002516
1.023379
SNP_A-1697748 1.625097 1.543559 1.543483 1.554699
0.616379
SNP_A-1699138 1.625097 1.543559 1.543483 1.554699
0.616379
SNP_A-1696782 2.365606 2.652155 2.582983 2.002516
1.398077
SNP_A-1750020 1.625097 1.543559 1.543483 1.554699
0.616379
SNP_A-1673422 2.365606 2.652155 2.582983 1.672339
1.398077
SNP_A-1670878 1.569111 1.53458 1.328269 1.672339 2.015989
SNP_A-1743511 1.569111 1.53458 1.328269 1.672339 2.015989
SNP_A-1646481 1.962492 1.929051 2.417274 1.554699
2.752331
SNP_A-1736635 1.569111 1.53458 1.328269 1.672339 3.106939
SNP_A-1666738 1.569111 1.53458 2.144473 1.672339 3.106939
SNP_A-1721407 1.569111 1.53458 2.144473 1.672339 3.106939
SNP_A-1686722 1.569111 1.53458 2.144473 1.672339 3.106939
SNP_A-1701882 1.962492 1.929051 2.417274 1.554699
2.752331
SNP_A-1701982 1.962492 1.929051 2.417274 1.554699
2.752331
SNP_A-1705703 2.207068 2.000052 2.144473 1.672339
3.106939
SNP_A-1737197 2.207068 2.000052 2.144473 1.672339
3.106939
SNP_A-1754224 2.207068 2.000052 2.144473 1.672339
3.106939
SNP_A-1749896 1.962492 1.929051 2.417274 1.554699
1.85133
SNP_A-1750090 1.962492 1.929051 2.417274 1.554699
1.85133
SNP_A-1642231 2.207068 2.000052 2.144473 1.672339
2.196275
SNP_A-1714480 1.962492 1.929051 2.417274 1.554699
1.85133
SNP_A-1712765 2.207068 2.000052 2.144473 1.672339
2.196275
SNP_A-1710770 2.207068 2.000052 2.144473 1.672339
1.518637
SNP_A-1649717 1.962492 1.929051 1.889378 1.554699
1.85133
SNP_A-1684884 2.207068 2.000052 2.144473 1.672339
1.518637
SNP_A-1658786 2.207068 2.000052 2.144473 1.672339
1.518637
SNP_A-1688090 2.207068 2.000052 2.144473 1.672339
1.518637
SNP_A-1703834 1.962492 1.929051 1.889378 1.554699
1.85133
SNP_A-1695724 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1645394 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1693756 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1680604 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1690704 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1665024 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1743269 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1703367 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1722718 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1677514 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1747841 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1737335 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1755813 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1670902 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1734642 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1747364 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1747266 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1747118 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1745353 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1745179 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1667036 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1667950 2.207068 2.000052 2.144473 1.672339
2.554806
SNP_A-1755067 1.962492 1.929051 1.889378 1.554699
2.469413
SNP_A-1740923 2.207068 2.513835 2.144473 1.672339
1.950623
SNP_A-1745466 2.207068 2.513835 2.144473 1.672339
1.950623
SNP_A-1703272 1.708302 1.929051 1.889378 1.554699
2.469413
SNP_A-1652197 1.708302 1.929051 1.889378 1.554699
2.469413
SNP_A-1739955 2.207068 2.513835 2.144473 1.672339
1.39178
SNP_A-1748063 2.207068 2.513835 2.144473 1.672339
1.39178
SNP_A-1705830 1.708302 1.929051 1.889378 1.554699
2.469413
SNP_A-1743804 1.708302 1.929051 1.889378 1.554699
2.469413
SNP_A-1744186 1.708302 1.929051 1.889378 1.554699
2.469413
SNP_A-1744304 1.708302 1.929051 1.889378 1.554699
2.469413
SNP_A-1698066 2.459832 1.929051 1.889378 1.554699
1.521922
SNP_A-1698244 2.459832 1.929051 1.889378 1.554699
1.521922
SNP_A-1743594 2.459832 1.929051 1.889378 1.554699
1.521922
SNP_A-1676349 2.459832 1.929051 1.889378 1.554699
1.521922
SNP_A-1656665 2.207068 2.002333 2.144473 1.672339
1.839669
SNP_A-1673751 1.795502 1.306216 1.553383 1.554699
2.854852
SNP_A-1755914 2.207068 2.002333 2.144473 1.672339
1.839669
SNP_A-1691957 2.297956 2.095738 2.054953 1.802846
1.850175
SNP_A-1699284 2.297956 2.095738 2.054953 1.802846
1.850175
SNP_A-1699392 2.297956 2.095738 2.054953 1.802846
1.850175
SNP_A-1676650 1.600346 2.002333 2.144473 1.672339
1.839669
SNP_A-1643131 1.600346 2.002333 2.144473 1.672339
1.839669
SNP_A-1684395 2.297956 2.697792 3.194801 1.802846
2.498451
SNP_A-1758748 1.600346 2.002333 2.144473 1.672339
1.839669
SNP_A-1698235 1.600346 2.002333 2.144473 1.672339
2.882365
SNP_A-1748913 2.439327 2.002333 2.144473 1.672339
2.882365
SNP_A-1683539 1.7659 1.524904 1.757271 1.463326 1.066465
SNP_A-1683663 1.7659 1.524904 1.757271 1.463326 1.066465
SNP_A-1680344 2.439327 2.546234 2.674752 1.933052
2.882365
PC1 PC2 PC3 PC4 PC5
SNP_A-1677174 1.683848 1.758366 2.355682 1.44551 1.359397
SNP_A-1718890 2.064341 2.054742 2.195673 2.071653
2.712994
SNP_A-1678466 2.192593 2.011548 2.169386 1.636554
1.121276
SNP_A-1676440 2.154233 2.007941 2.163353 1.619221
1.097597
SNP_A-1662392 2.105124 1.97601 2.128437 1.597088 1.077265
SNP_A-1685736 2.104064 1.975642 2.128008 1.596684
1.076653
SNP_A-1681384 2.06087 1.959299 2.109115 1.579172 1.053125
SNP_A-1668776 2.073088 2.1996 2.232535 1.666137 0.462655
SNP_A-1642581 1.598771 1.396639 1.55226 1.132458 1.194469
SNP_A-1669029 1.575062 1.368512 1.52632 1.110835 1.238995
SNP_A-1723597 1.985052 1.953741 2.128644 1.519188
0.449499
SNP_A-1718237 1.546209 1.230899 1.393048 1.016112
1.423954
SNP_A-1748467 1.546363 1.230625 1.392818 1.015973
1.424737
SNP_A-1728870 1.979467 1.899551 2.115747 1.491868
0.461822
SNP_A-1669946 2.056022 1.852391 2.187254 1.506121
0.609066
SNP_A-1708099 2.058574 1.854326 2.189889 1.508143
0.612346
SNP_A-1716798 2.114055 1.899741 2.250672 1.554699
0.691504
SNP_A-1701872 2.120698 2.065504 2.411059 1.660034
0.620438
SNP_A-1705537 2.365582 2.675569 2.61206 2.002685 1.023177
SNP_A-1683756 2.365629 2.675456 2.611955 2.002516
1.023581
SNP_A-1697748 1.625203 1.543781 1.543728 1.309819
1.047963
SNP_A-1699138 1.625097 1.543559 1.543483 1.309776
1.048499
SNP_A-1696782 2.404167 2.629058 2.554334 1.905737
1.300316
SNP_A-1750020 1.60325 1.506301 1.499031 1.298324 1.133321
SNP_A-1673422 2.099086 2.2876 2.262198 1.697266 1.50319
SNP_A-1670878 1.166049 1.226503 1.328269 1.115131
2.015895
SNP_A-1743511 1.166064 1.226408 1.328193 1.115115
2.016084
SNP_A-1646481 2.346815 2.494283 2.676267 1.535596
2.714153
SNP_A-1736635 1.443353 1.372964 1.450476 1.274043
2.618858
SNP_A-1666738 1.73145 1.742521 1.968976 1.565212 3.392383
SNP_A-1721407 1.705825 1.715222 1.989342 1.548463
3.510922
SNP_A-1686722 1.722203 1.724465 2.059079 1.575875
3.555464
SNP_A-1701882 2.144818 1.872208 2.311115 1.656525
2.753629
SNP_A-1701982 2.144926 1.872441 2.311192 1.656562
2.752331
SNP_A-1705703 2.184358 1.784769 2.089551 1.617257
3.106939
SNP_A-1737197 2.256938 1.834004 2.087989 1.635547
2.730668
SNP_A-1754224 2.321849 1.866 2.092987 1.65512 2.650839
SNP_A-1749896 2.256507 2.095352 2.416895 1.701413
1.854551
SNP_A-1750090 2.257145 2.096511 2.417651 1.701709
1.85133
SNP_A-1642231 2.316252 1.912153 2.118652 1.658918
2.302816
SNP_A-1714480 2.327411 2.213575 2.512774 1.737442
1.587623
SNP_A-1712765 2.281268 1.92863 2.129137 1.658291 2.094664
SNP_A-1710770 2.031017 1.963167 2.096597 1.656886
1.419065
SNP_A-1649717 1.944866 2.069094 1.979491 1.707225
1.719089
SNP_A-1684884 1.776255 1.849903 1.823619 1.606647
1.518027
SNP_A-1658786 1.776354 1.849566 1.823381 1.60646 1.519248
SNP_A-1688090 1.776566 1.848819 1.822858 1.606045
1.521938
SNP_A-1703834 2.069708 2.051761 2.103292 1.643174
1.913919
SNP_A-1695724 2.047037 2.04666 2.091564 1.551024 2.382883
SNP_A-1645394 2.11638 1.975569 2.205808 1.742888 2.960586
SNP_A-1693756 1.980278 2.01199 2.036653 1.528688 2.497495
SNP_A-1680604 2.18573 2.01009 2.273021 1.738643 2.93149
SNP_A-1690704 1.924566 1.955514 1.987214 1.511749
2.482347
SNP_A-1665024 2.205516 2.027664 2.273461 1.725739
2.742915
SNP_A-1743269 2.20862 2.028513 2.271614 1.7204 2.708789
SNP_A-1703367 2.20865 2.028518 2.271594 1.720343 2.708451
SNP_A-1722718 2.209393 2.028617 2.271052 1.718885
2.699981
SNP_A-1677514 2.220356 2.024038 2.257394 1.687132
2.554806
SNP_A-1747841 2.220485 2.023896 2.257151 1.68661 2.552765
SNP_A-1737335 2.220533 2.023844 2.257063 1.686419
2.552026
SNP_A-1755813 1.81457 1.839007 1.894196 1.472597 2.507589
SNP_A-1670902 2.223593 2.019571 2.250477 1.67249 2.499873
SNP_A-1734642 2.223654 2.019468 2.250331 1.672186
2.498773
SNP_A-1747364 1.80425 1.821152 1.884572 1.469245 2.479934
SNP_A-1747266 1.804186 1.821025 1.88451 1.469226 2.479687
SNP_A-1747118 1.80405 1.820755 1.884376 1.469184 2.479154
SNP_A-1745353 1.8019 1.816321 1.882239 1.468535 2.469873
SNP_A-1745179 1.801709 1.815905 1.882045 1.468479
2.468952
SNP_A-1667036 2.240187 2.00773 2.23144 1.617593 2.257955
SNP_A-1667950 2.239395 1.992403 2.216495 1.593016
2.195094
SNP_A-1755067 1.782379 1.72549 1.846195 1.463445 2.125435
SNP_A-1740923 2.039624 2.415264 2.15992 1.730608 2.00664
SNP_A-1745466 2.025471 2.438556 2.177265 1.72224 1.896169
SNP_A-1703272 1.775209 2.02944 1.986413 1.727083 2.503907
SNP_A-1652197 1.735071 1.902945 1.796525 1.618895
2.361615
SNP_A-1739955 1.977627 2.591436 2.289956 1.690912
1.393028
SNP_A-1748063 1.977469 2.592448 2.290694 1.690791
1.390534
SNP_A-1705830 1.709983 1.845484 1.713831 1.56642 2.288484
SNP_A-1743804 1.706624 1.838465 1.703885 1.559863
2.279153
SNP_A-1744186 1.705866 1.836902 1.701673 1.558397
2.277061
SNP_A-1744304 1.70584 1.836846 1.701595 1.558345 2.276987
SNP_A-1698066 2.459895 2.049176 2.271816 1.771057
1.579532
SNP_A-1698244 2.459895 2.049971 2.271781 1.771811
1.576904
SNP_A-1743594 2.459771 2.082588 2.269699 1.803766
1.468857
SNP_A-1676349 2.459 2.137081 2.263041 1.862457 1.286784
SNP_A-1656665 1.786321 2.002333 1.986631 1.614152
2.275914
SNP_A-1673751 1.795502 1.306216 1.553383 1.252368
2.854852
SNP_A-1755914 1.783371 2.007073 1.96485 1.603998 2.399841
SNP_A-1691957 2.239522 2.026019 1.953517 1.751819
1.790003
SNP_A-1699284 2.297943 2.095738 2.054953 1.802837
1.850175
SNP_A-1699392 2.297967 2.095767 2.054989 1.802856
1.850196
SNP_A-1676650 1.572419 1.709425 2.076751 1.759038
1.736321
SNP_A-1643131 1.598041 1.755454 2.085867 1.757031
1.819656
SNP_A-1684395 2.78649 2.697792 3.194801 2.282217 2.498451
SNP_A-1758748 1.602654 1.766084 2.087448 1.755133
1.839669
SNP_A-1698235 1.738626 2.020004 2.160402 1.710735
2.713329
SNP_A-1748913 2.229433 2.218839 2.088084 1.702811
5.120838
SNP_A-1683539 1.766341 1.524746 1.757299 1.463427
1.066172
SNP_A-1683663 1.7659 1.524904 1.757271 1.463326 1.066465
SNP_A-1680344 2.445945 2.28263 2.327505 1.855074 3.447962
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