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Sample GSM90753 Query DataSets for GSM90753
Status Public on Jan 06, 2006
Title GORILLA 1 [HSR (human female) vs. NG05251 (Gorilla male 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 Gorilla male cell line genomic DNA
Organism Homo sapiens
Characteristics Gorilla male 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/2002-11/35158.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 1524 1703 323 516 1201 1187 1415 1676 329 551 1092 1160 0 0 721 624 110 248 93 93 90 84 2388 2252 1.012 .988 1.062 1.133 .931 2.611 32 164 .969 .79 60 2380 7290 74 80 67 73 0 2077 629 1448 1.205 2044 1415 .83 1.295 .269 .373
2 3079 3224 324 494 2755 2730 2909 3011 388 525 2585 2517 0 0 1373 1198 832 234 93 100 71 100 5485 5102 1.009 .991 .974 1.028 .984 1.625 32 216 .987 .86 70 2530 7290 73 80 81 88 0 3932 602 3329 1.208 3672 3070 .828 1.187 .273 .248
3 1659 1363 355 468 1304 895 1643 1203 368 512 1288 735 0 0 425 349 71 195 100 100 100 100 2199 2023 1.457 .686 .571 .678 .64 1.312 12 68 .659 .72 40 2680 7290 75 79 98 102 0 1662 571 1091 .837 1467 896 1.195 .696 -.257 -.523
4 1610 1588 357 462 1253 1126 1817 1719 395 494 1460 1257 0 0 833 442 148 177 91 100 91 91 2379 2717 1.113 .899 .861 .876 .91 1.528 12 98 .673 .72 50 2820 7280 73 78 111 116 0 1937 563 1373 1.096 2096 1533 .912 1.05 .132 .07
5 3368 2693 324 451 3044 2242 3402 2628 343 478 3078 2177 0 0 1160 1051 133 217 100 100 100 100 5286 5255 1.358 .737 .707 .708 .746 1.529 32 216 .743 .83 70 2960 7300 74 81 124 131 0 3284 550 2734 .898 3205 2655 1.113 .863 -.155 -.213
6 2712 2191 319 463 2393 1728 2522 2172 329 475 2203 1709 0 0 839 740 121 162 100 100 100 100 4121 3912 1.385 .722 .776 .702 .7 1.416 32 227 .727 .9 70 3120 7290 73 80 140 147 0 2672 565 2107 .881 2649 2084 1.136 .946 -.183 -.08
7 2357 1624 323 471 2034 1153 2399 1764 326 491 2076 1293 0 0 1340 469 79 186 96 96 96 93 3187 3369 1.764 .567 .623 .665 .627 2.077 32 176 .441 .65 60 3260 7290 74 80 155 161 0 1980 574 1406 .691 2151 1577 1.447 .76 -.533 -.397
8 2160 1959 318 470 1842 1489 2081 1895 325 503 1763 1425 0 0 670 642 91 213 100 100 100 100 3331 3188 1.237 .808 .808 .79 .793 1.527 32 204 .815 .87 70 3410 7290 73 80 169 176 0 2389 573 1816 .986 2311 1738 1.014 .986 -.021 -.021
9 2401 2033 304 475 2097 1558 2504 2127 318 501 2200 1652 0 0 699 690 88 191 100 98 100 94 3655 3852 1.346 .743 .751 .693 .767 1.771 52 338 .777 .85 90 3540 7290 72 81 181 190 0 2479 579 1900 .906 2594 2015 1.104 .916 -.142 -.127
10 1142 996 314 453 828 543 1207 996 321 497 893 543 0 0 427 285 85 187 93 87 93 65 1371 1436 1.525 .656 .608 .6 .632 2.138 32 164 .621 .73 60 3700 7290 74 80 199 205 0 1215 552 662 .8 1215 662 1.25 .742 -.322 -.431
11 1875 1803 310 479 1565 1324 1875 1754 322 504 1565 1275 0 0 529 741 84 188 100 100 100 96 2889 2840 1.182 .846 .815 .813 .812 1.596 52 332 .944 .79 90 3840 7290 72 81 211 220 0 2199 584 1615 1.032 2139 1555 .969 .994 .045 -.009
12 1611 1647 320 486 1291 1161 1660 1413 325 506 1340 927 0 0 617 862 78 175 100 98 100 92 2452 2267 1.112 .899 .692 .823 .853 2.038 52 276 1.074 .71 80 3990 7290 73 81 227 235 0 2009 593 1416 1.097 1723 1130 .912 .844 .133 -.245
13 2202 2276 304 461 1898 1815 2023 2228 307 497 1719 1767 0 0 965 885 71 201 100 100 100 100 3713 3486 1.046 .956 1.028 .944 1.008 1.492 52 275 .921 .88 90 4140 7280 71 80 241 250 0 2776 562 2213 1.166 2717 2155 .857 1.254 .222 .326
14 2879 2182 289 443 2590 1739 3056 2204 298 464 2767 1761 0 0 1040 719 72 172 100 99 99 99 4329 4528 1.489 .671 .636 .686 .705 1.786 120 441 .668 .91 120 4270 7290 71 83 253 265 0 2661 540 2121 .819 2688 2148 1.221 .776 -.288 -.366
15 1960 1432 292 457 1668 975 2006 1385 296 474 1714 928 0 0 496 408 61 169 100 100 100 100 2643 2642 1.711 .585 .541 .561 .583 1.397 80 291 .605 .89 100 4420 7290 72 82 269 279 0 1746 557 1189 .713 1689 1132 1.403 .66 -.488 -.599
16 8586 8082 292 445 8294 7637 8401 7669 294 462 8109 7224 0 0 4315 3672 63 174 97 100 97 100 15931 15333 1.086 .921 .891 1.01 .934 2.221 120 416 .893 .93 120 4560 7290 71 83 282 294 0 9856 543 9313 1.123 9352 8810 .891 1.086 .167 .12
17 2946 3152 290 396 2656 2756 2976 3126 316 442 2686 2730 0 0 937 894 287 375 98 97 97 96 5412 5416 .964 1.038 1.016 1.073 1.057 1.839 120 469 1.039 .9 120 4700 7290 71 83 296 308 0 3844 483 3361 1.265 3812 3329 .79 1.239 .34 .31
18 429 595 296 431 133 164 325 471 307 451 29 40 0 0 291 352 70 152 32 32 21 28 297 69 .811 1.233 1.379 1.412 1.371 4.185 52 227 1.515 .44 80 4860 7280 72 80 314 322 -50 726 526 200 1.504 574 49 .665 1.682 .589 .75
19 6099 5233 301 461 5798 4772 5521 5149 306 471 5220 4688 0 0 3670 2870 65 147 97 94 97 92 10570 9908 1.215 .823 .898 .841 .86 2.538 120 446 .783 .88 120 5010 7290 71 83 327 339 0 6382 562 5820 1.004 6279 5717 .996 1.095 .005 .131
20 2436 1990 297 456 2139 1534 2443 1966 301 466 2146 1510 0 0 607 446 64 147 100 100 100 100 3673 3656 1.394 .717 .704 .716 .727 1.396 80 308 .711 .88 100 5140 7290 72 82 341 351 0 2427 556 1871 .875 2398 1841 1.143 .858 -.193 -.221

Total number of rows: 43008

Table truncated, full table size 10030 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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