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Sample GSM90768 Query DataSets for GSM90768
Status Public on Jan 06, 2006
Title ORANG 3 [HSR (human female) vs. LA27 (Orangutan female)]
Sample type genomic
 
Channel 1
Source name Human female genomic DNA
Organism Homo sapiens
Characteristics Human female genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Orangutan female genomic DNA
Organism Homo sapiens
Characteristics Orangutan female genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40423.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 05, 2006
Last update date Feb 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3310
Series (2)
GSE3980 Lineage-specific gene duplication and loss in human and great ape evolution
GSE9028 Extended Primate aCGH

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 383 562 87 126 296 436 341 693 92 133 254 567 0 0 172 250 25 46 100 100 100 100 732 821 .679 1.473 2.232 1.418 1.357 1.47 12 98 1.782 .86 50 2390 7200 77 82 76 81 0 737 165 571 1.931 908 743 .518 2.926 .949 1.549
2 612 739 85 127 527 612 603 790 88 130 518 663 0 0 203 276 22 51 100 96 100 96 1139 1181 .861 1.161 1.28 1.131 1.303 1.461 32 189 1.263 .91 70 2530 7230 79 86 89 96 0 969 166 802 1.522 1035 869 .657 1.678 .606 .746
3 145 230 86 123 59 107 93 149 87 129 7 26 0 0 139 225 22 49 33 33 25 23 166 33 .551 1.814 3.714 1.685 1.495 3.335 80 425 1.905 .84 100 2660 7210 76 86 101 111 -100 301 161 140 2.377 195 34 .421 4.868 1.249 2.283
4 295 477 88 123 207 354 297 503 89 130 209 380 0 0 130 193 21 47 90 90 84 87 561 589 .585 1.71 1.818 1.842 1.612 2.175 32 167 1.766 .87 60 2830 7210 78 84 120 126 0 625 161 464 2.241 659 498 .446 2.383 1.164 1.253
5 611 643 91 126 520 517 623 592 108 146 532 466 0 0 257 298 82 83 92 92 90 84 1037 998 1.006 .994 .876 .965 1.06 1.861 52 309 1.05 .92 80 2980 7220 78 86 134 142 0 843 165 678 1.303 776 611 .767 1.148 .382 .199
6 536 725 87 134 449 591 552 740 99 148 465 606 0 0 159 229 70 90 100 100 96 96 1040 1071 .76 1.316 1.303 1.298 1.25 1.412 32 170 1.4 .93 60 3120 7220 79 85 149 155 0 950 176 775 1.725 970 794 .58 1.708 .787 .772
7 470 595 84 136 386 459 479 574 87 143 395 438 0 0 200 231 21 54 100 96 96 96 845 833 .841 1.189 1.109 1.253 1.358 1.5 32 200 1.215 .91 70 3260 7220 78 85 162 169 0 780 178 602 1.559 752 574 .642 1.453 .64 .539
8 529 600 90 133 439 467 521 612 92 142 431 479 0 0 182 223 23 56 96 96 96 96 906 910 .94 1.064 1.111 1.039 1.022 1.41 32 170 1.113 .91 60 3400 7210 78 84 177 183 0 786 174 612 1.394 802 628 .717 1.457 .48 .543
9 494 464 92 138 402 326 497 458 93 143 405 320 0 0 112 124 21 51 100 100 100 96 728 725 1.233 .811 .79 .78 .847 1.521 52 280 .824 .86 80 3540 7210 77 85 190 198 0 608 181 427 1.063 600 419 .941 1.036 .088 .05
10 276 429 91 134 185 295 284 432 92 137 193 298 0 0 110 192 21 46 90 90 90 81 480 491 .627 1.595 1.544 1.538 1.835 2.641 32 166 1.848 .84 60 3690 7210 78 84 206 212 0 562 176 387 2.09 566 391 .478 2.024 1.064 1.017
11 378 376 88 138 290 238 382 373 89 145 294 235 0 0 118 117 21 51 100 94 100 88 528 529 1.218 .821 .799 .777 .785 1.726 52 288 .831 .81 90 3830 7220 77 86 218 227 0 493 181 312 1.076 489 308 .93 1.048 .105 .067
12 399 423 85 133 314 290 386 423 87 137 301 290 0 0 156 150 23 49 98 96 93 90 604 591 1.083 .924 .963 .955 .92 1.765 80 367 .94 .88 100 3970 7210 76 86 232 242 0 554 174 380 1.21 554 380 .826 1.263 .276 .337
13 609 682 87 135 522 547 583 684 89 138 496 549 0 0 222 197 22 50 100 100 100 100 1069 1045 .954 1.048 1.107 1.084 1.061 1.345 52 264 .996 .93 90 4120 7210 76 85 247 256 0 894 177 717 1.373 897 720 .728 1.451 .458 .537
14 785 701 86 122 699 579 820 714 92 135 734 592 0 0 240 192 42 60 100 100 100 98 1278 1326 1.207 .828 .807 .833 .828 1.33 80 316 .818 .94 100 4260 7210 76 86 261 271 0 919 160 759 1.086 936 776 .921 1.057 .119 .08
15 452 397 87 120 365 277 452 399 96 133 365 279 0 0 72 85 47 60 100 100 100 97 642 644 1.318 .759 .764 .737 .781 1.461 80 290 .754 .85 100 4410 7210 76 86 276 286 0 520 157 363 .995 523 366 1.005 1.002 -.008 .003
16 1265 1247 85 117 1180 1130 1373 1302 89 124 1288 1185 0 0 941 812 25 46 90 95 88 93 2310 2473 1.044 .958 .92 1.235 .972 2.162 120 443 .909 .98 120 4550 7220 76 88 289 301 0 1634 153 1481 1.255 1706 1553 .797 1.206 .328 .27
17 758 677 86 118 672 559 743 668 93 121 657 550 0 0 184 167 41 39 100 100 100 100 1231 1207 1.202 .832 .837 .825 .834 1.324 80 323 .851 .94 100 4690 7210 76 86 304 314 0 887 155 733 1.09 876 721 .917 1.097 .125 .134
18 114 163 91 129 23 34 103 133 97 136 12 4 0 0 50 97 42 48 15 28 7 16 57 16 .676 1.478 .333 1.759 1.667 3.312 80 346 2.506 .35 100 4850 7200 75 85 320 330 -50 214 169 45 1.938 174 5 .516 .437 .954 -1.195
19 1240 1045 92 139 1148 906 1048 966 96 147 956 827 0 0 768 557 29 60 98 97 98 96 2054 1783 1.267 .789 .865 .816 .801 1.407 80 309 .761 .95 100 5000 7210 76 86 335 345 0 1370 182 1187 1.034 1266 1084 .967 1.134 .049 .181
20 617 470 93 132 524 338 629 464 99 143 536 332 0 0 160 136 45 60 100 100 100 97 862 868 1.55 .645 .619 .63 .636 1.498 80 314 .667 .87 100 5140 7210 76 86 349 359 0 616 173 443 .845 608 435 1.183 .812 -.242 -.301

Total number of rows: 43008

Table truncated, full table size 9500 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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