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Sample GSM90757 Query DataSets for GSM90757
Status Public on Jan 06, 2006
Title ORANG 2 [HSR (human female) vs. NG06209 (Orangutan female cell line)]
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 cell line genomic DNA
Organism Homo sapiens
Characteristics Orangutan female cell line genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37968.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 GPL1448
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
1 416 518 128 177 288 341 398 517 128 182 270 340 0 0 138 127 33 59 93 96 93 96 629 610 .845 1.184 1.259 1.184 1.113 1.904 32 163 1.157 .78 60 2190 7180 75 81 64 70 0 581 198 382 1.327 579 381 .754 1.411 .408 .497
2 676 765 128 176 548 589 658 735 128 187 530 559 0 0 315 243 32 66 98 98 94 98 1137 1089 .93 1.075 1.055 1.207 1.065 1.982 52 206 .965 .87 80 2330 7180 74 82 77 85 0 857 197 660 1.205 824 627 .83 1.182 .269 .241
3 176 270 125 184 51 86 129 209 126 193 4 25 0 0 141 205 35 63 26 33 15 18 137 29 .593 1.686 6.25 2.108 1.983 2.603 80 371 1.499 .78 100 2440 7170 72 82 87 97 -50 303 206 96 1.89 234 28 .529 7.005 .918 2.808
4 475 621 126 196 349 425 511 593 124 204 385 397 0 0 124 222 29 63 100 100 100 100 774 782 .821 1.218 1.031 1.14 1.094 1.291 12 98 1.485 .86 50 2620 7160 73 78 107 112 0 696 220 476 1.365 665 445 .733 1.156 .449 .209
5 1240 1461 124 174 1116 1287 1344 1496 124 182 1220 1322 0 0 353 368 33 68 100 100 100 100 2403 2542 .867 1.153 1.084 1.167 1.241 1.394 32 205 1.167 .89 70 2760 7180 74 81 120 127 0 1638 195 1443 1.293 1677 1482 .774 1.215 .37 .28
6 790 843 121 181 669 662 800 864 122 188 679 683 0 0 376 383 31 66 98 94 92 86 1331 1362 1.011 .99 1.006 .996 .952 1.886 52 259 1 .85 80 2900 7180 74 82 134 142 0 945 203 742 1.109 968 766 .902 1.127 .149 .173
7 744 827 127 188 617 639 775 840 127 189 648 652 0 0 253 231 33 59 100 100 100 96 1256 1300 .966 1.036 1.006 1.057 .974 1.776 32 148 1.013 .86 60 3070 7170 74 80 152 158 0 927 211 716 1.161 942 731 .861 1.128 .215 .173
8 839 873 129 186 710 687 813 855 133 198 684 669 0 0 405 332 57 73 93 100 93 100 1397 1353 1.033 .968 .978 1.079 .946 1.864 32 177 .899 .93 70 3170 7160 72 79 161 168 0 979 208 770 1.085 958 750 .922 1.096 .117 .133
9 807 794 124 200 683 594 797 777 129 210 673 577 0 0 181 164 48 71 100 100 100 100 1277 1250 1.15 .87 .857 .868 .837 1.407 80 367 .866 .89 100 3320 7170 72 82 175 185 0 890 224 666 .975 871 647 1.026 .961 -.037 -.057
10 310 361 126 202 184 159 317 344 128 209 191 142 0 0 85 102 35 72 96 82 88 48 343 333 1.157 .864 .743 .805 .825 2.528 80 299 1.055 .6 100 3470 7170 72 82 190 200 0 405 226 178 .969 386 159 1.032 .833 -.046 -.263
11 720 772 121 211 599 561 713 753 126 213 592 542 0 0 146 150 35 64 100 100 100 100 1160 1134 1.068 .937 .916 .932 .924 1.423 80 294 .945 .88 100 3610 7170 72 82 204 214 0 865 237 629 1.05 844 608 .953 1.026 .07 .037
12 543 630 122 200 421 430 530 602 124 205 408 402 0 0 170 187 33 63 100 100 100 100 851 810 .979 1.021 .985 1.014 1.017 1.628 80 314 1.071 .82 100 3760 7170 72 82 219 229 0 706 224 482 1.145 675 451 .874 1.104 .195 .143
13 901 911 123 200 778 711 896 914 125 203 773 714 0 0 233 223 32 63 100 100 100 100 1489 1487 1.094 .914 .924 .908 .921 1.436 80 307 .913 .91 100 3910 7170 72 82 234 244 0 1021 224 797 1.024 1024 800 .976 1.035 .035 .05
14 866 776 121 192 745 584 843 735 125 200 722 543 0 0 252 229 36 62 100 100 100 100 1329 1265 1.276 .784 .752 .782 .757 1.603 80 332 .78 .85 100 4050 7170 72 82 248 258 0 870 215 655 .879 824 609 1.138 .843 -.187 -.246
15 530 576 122 195 408 381 525 560 125 200 403 365 0 0 108 126 37 56 100 100 100 100 789 768 1.071 .934 .906 .915 .893 1.417 80 314 .952 .86 100 4200 7170 72 82 263 273 0 646 219 427 1.047 628 409 .955 1.015 .066 .022
16 142 216 123 191 19 25 130 201 125 194 7 10 0 0 75 79 31 62 26 21 13 8 44 17 .76 1.316 1.429 1.489 1.541 4.381 80 329 3.492 .19 100 4340 7160 71 81 277 287 -50 242 214 28 1.475 225 11 .678 1.601 .561 .679
17 1309 1496 120 184 1189 1312 1322 1491 121 188 1202 1307 0 0 454 326 31 61 100 100 100 100 2501 2509 .906 1.103 1.087 1.168 1.138 1.508 80 297 1.058 .91 100 4490 7170 72 82 292 302 0 1677 206 1471 1.237 1671 1465 .809 1.219 .307 .285
18 140 201 119 189 21 12 128 192 123 199 9 3 0 0 75 79 37 67 22 21 8 5 33 12 1.75 .571 .333 2.342 2.704 3.194 80 313 2.002 .42 100 4630 7160 71 81 306 316 -50 225 212 13 .64 215 3 1.561 .374 -.643 -1.42
19 3342 3091 118 198 3224 2893 3250 3168 123 207 3132 2970 0 0 1136 745 40 74 100 100 100 100 6117 6102 1.114 .897 .948 .93 .891 1.32 80 315 .85 .95 100 4780 7170 72 82 321 331 0 3465 222 3243 1.006 3551 3329 .994 1.063 .008 .088
20 681 635 113 183 568 452 685 621 117 189 572 438 0 0 221 155 33 62 98 100 97 100 1020 1010 1.257 .796 .766 .867 .826 2.065 80 294 .751 .84 100 4930 7170 72 82 336 346 0 712 205 507 .892 696 491 1.121 .858 -.165 -.22

Total number of rows: 43104

Table truncated, full table size 9792 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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