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Sample GSM229016 Query DataSets for GSM229016
Status Public on Feb 24, 2012
Title Macaque #487
Sample type genomic
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Test
Organism Macaca sp.
Characteristics Test
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Comparative genomics, DNA
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 Sep 12, 2007
Last update date Feb 24, 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 GPL5846
Series (1)
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
1 496 197 144 107 352 90 455 179 147 114 311 72 0 0 160 97 49 54 100 54 100 35 442 383 3.911 .256 .232 .29 .26 .17 26 480 .43 .94 50 2710 6440 85 90 68 73 0 248 134 113 .321 225 90 3.112 .291 -1.638 -1.781
2 703 444 139 107 564 337 629 370 143 114 490 263 0 0 263 206 50 54 100 95 100 90 901 753 1.674 .598 .537 .59 .6 .23 21 451 .63 .98 50 2850 6440 85 90 82 87 0 558 134 424 .751 465 331 1.332 .675 -.413 -.568
3 1157 471 139 108 1018 363 1218 508 176 143 1079 400 0 0 385 237 424 284 90 62 71 24 1381 1479 2.804 .357 .371 .35 .34 .17 21 470 .41 .98 50 2990 6440 85 90 96 101 0 592 136 456 .448 638 503 2.231 .466 -1.158 -1.102
4 831 354 141 108 690 246 830 350 178 140 689 242 0 0 174 105 424 284 90 33 19 0 936 931 2.805 .357 .351 .36 .36 .17 21 471 .44 .98 50 3140 6440 85 90 111 116 0 445 136 309 .448 440 304 2.232 .441 -1.158 -1.18
5 470 259 140 104 330 155 478 263 142 111 338 159 0 0 204 111 34 52 97 77 87 65 485 497 2.129 .47 .47 .52 .39 .39 31 448 .57 .98 60 3280 6440 85 91 125 131 0 325 131 195 .59 331 200 1.694 .591 -.76 -.758
6 1201 666 137 108 1064 558 1170 595 140 111 1033 487 0 0 426 311 34 54 100 96 100 92 1622 1520 1.907 .524 .471 .54 .5 .3 26 449 .57 .98 50 3430 6440 85 90 140 145 0 837 136 701 .659 748 612 1.517 .592 -.601 -.755
7 854 576 138 111 716 465 823 506 140 116 685 395 0 0 303 281 33 58 100 100 100 100 1181 1080 1.54 .649 .577 .65 .53 .3 21 459 .69 .99 50 3570 6440 85 90 154 159 0 724 139 584 .816 636 496 1.225 .725 -.293 -.465
8 770 417 138 110 632 307 811 396 139 118 673 286 0 0 274 179 33 57 100 94 100 88 939 959 2.059 .486 .425 .56 .44 .36 32 420 .54 .98 60 3720 6440 85 91 169 175 0 524 138 386 .61 498 359 1.638 .534 -.712 -.905
9 499 280 139 111 360 169 515 282 140 120 376 171 0 0 145 100 31 58 100 84 93 70 529 547 2.13 .469 .455 .69 .42 .95 44 427 .57 .95 70 3870 6440 84 91 183 190 0 352 139 212 .59 354 215 1.695 .572 -.761 -.807
10 1165 807 137 108 1028 699 1243 764 140 120 1106 656 0 0 349 339 34 60 100 100 100 94 1727 1762 1.471 .68 .593 .67 .66 .27 34 400 .7 .99 60 4020 6420 83 89 199 205 0 1014 136 878 .855 960 824 1.17 .745 -.227 -.424
11 281 190 137 99 144 91 278 189 138 108 141 90 0 0 54 68 31 50 99 73 95 44 235 231 1.582 .632 .638 .82 .68 .67 112 323 .69 .94 120 4170 6410 79 91 211 223 0 239 124 114 .794 238 113 1.259 .802 -.332 -.318
12 799 481 136 109 663 372 824 480 138 116 688 371 0 0 227 157 32 56 97 97 97 91 1035 1059 1.782 .561 .539 .76 .57 .75 34 423 .61 .98 60 4320 6400 81 87 229 235 0 604 137 468 .705 603 466 1.418 .678 -.504 -.561
13 615 470 132 116 483 354 633 506 134 123 501 390 0 0 176 146 33 61 100 94 100 91 837 891 1.364 .733 .778 .8 .74 .51 32 429 .75 .98 60 4470 6410 82 88 244 250 0 591 146 445 .921 636 490 1.086 .978 -.119 -.032
14 1256 1102 127 104 1129 998 1265 1066 130 114 1138 962 0 0 353 455 32 57 100 100 100 98 2127 2100 1.131 .884 .845 .87 .84 .31 44 406 .89 .99 70 4610 6410 81 88 257 264 0 1385 131 1254 1.111 1340 1209 .9 1.062 .152 .087
15 414 244 127 102 287 142 458 232 131 112 331 130 0 0 137 91 35 56 97 82 88 62 429 461 2.021 .495 .393 .59 .4 .53 34 434 .61 .96 60 4740 6410 82 88 271 277 0 307 128 178 .622 292 163 1.608 .494 -.685 -1.019
16 1564 773 132 108 1432 665 1501 797 133 118 1369 689 0 0 832 379 31 58 100 94 100 88 2097 2058 2.153 .464 .503 .55 .49 .31 32 457 .49 .98 60 4900 6410 82 88 287 293 0 971 136 836 .584 1002 866 1.713 .633 -.777 -.661
17 819 489 127 109 692 380 824 489 131 118 697 380 0 0 189 166 33 56 100 100 100 96 1072 1077 1.821 .549 .545 .54 .53 .19 26 455 .61 .99 50 5040 6410 82 87 301 306 0 615 137 478 .69 615 478 1.449 .685 -.535 -.545
18 844 631 125 114 719 517 889 607 128 123 764 493 0 0 203 204 33 59 100 98 100 95 1236 1257 1.391 .719 .645 .72 .71 .26 44 445 .76 .99 70 5190 6400 80 87 315 322 0 793 143 650 .904 763 620 1.107 .811 -.146 -.302
19 2763 1497 130 118 2633 1379 2748 1478 133 125 2618 1360 0 0 422 429 37 60 100 100 100 100 4012 3978 1.909 .524 .519 .51 .5 .13 37 431 .55 .99 70 5330 6410 81 88 329 336 0 1881 148 1733 .658 1857 1709 1.519 .653 -.603 -.615
20 622 386 125 106 497 280 623 419 128 112 498 313 0 0 103 137 35 53 100 93 100 89 777 811 1.775 .563 .629 .56 .6 .24 44 424 .64 .98 70 5480 6410 81 88 344 351 0 485 133 352 .708 527 393 1.412 .79 -.498 -.34

Total number of rows: 43008

Table truncated, full table size 9501 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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