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Sample GSM229019 Query DataSets for GSM229019
Status Public on Feb 24, 2012
Title shgc155|PR00338 Lemur
Sample type genomic
 
Channel 1
Source name Normal human male genomic DNA
Organism Homo sapiens
Characteristics Normal human male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Lemur genomic DNA
Organism Lemur sp.
Characteristics Lemur genomic DNA
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, aCGH cell line
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) [email protected]
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 GPL5845
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 1418 1196 189 318 1229 878 1445 1108 194 346 1256 790 0 0 358 479 69 212 100 96 100 81 2107 2046 1.4 .714 .629 .75 .63 .46 69 437 .87 .97 90 2280 6040 43 52 31 40 0 1749 465 1284 1.045 1621 1155 .957 .92 .063 -.12
2 2223 1486 202 343 2021 1143 2110 1194 204 376 1908 851 0 0 884 1320 73 223 100 87 100 72 3164 2759 1.768 .566 .446 .5 .45 .28 60 368 .7 .94 80 2440 6050 45 53 48 56 0 2173 502 1672 .827 1746 1245 1.209 .652 -.274 -.616
3 2545 2586 207 323 2338 2263 2418 2335 212 370 2211 2012 0 0 843 1275 75 228 100 100 100 96 4601 4223 1.033 .968 .91 .92 .92 .33 52 366 1.01 .98 80 2580 6050 45 53 62 70 0 3782 472 3310 1.416 3415 2943 .706 1.331 .501 .412
4 2337 1305 188 332 2149 973 2160 1140 198 362 1972 808 0 0 788 679 70 220 100 90 100 81 3122 2780 2.209 .453 .41 .44 .43 .25 52 362 .57 .98 80 2730 6050 45 53 77 85 0 1909 486 1423 .662 1667 1182 1.51 .599 -.595 -.739
5 1010 819 186 329 824 490 1015 800 193 367 829 471 0 0 295 352 67 226 99 74 97 51 1314 1300 1.682 .595 .568 .73 .64 .67 69 377 .84 .96 90 2850 6050 44 53 88 97 0 1198 481 717 .87 1170 689 1.15 .831 -.201 -.267
6 2632 1857 198 330 2434 1527 2405 1711 209 368 2207 1381 0 0 824 982 79 232 100 97 100 95 3961 3588 1.594 .627 .626 .59 .57 .27 37 416 .73 .98 70 3020 6050 45 52 106 113 0 2716 483 2233 .918 2502 2020 1.09 .915 -.124 -.128
7 1546 689 211 355 1335 334 1483 665 224 383 1272 310 0 0 278 326 85 243 100 57 100 24 1669 1582 3.997 .25 .244 .31 .27 .2 70 320 .45 .91 90 3160 6050 44 53 119 128 0 1008 519 488 .366 973 453 2.733 .356 -1.45 -1.488
8 2063 1078 194 364 1869 714 2054 1000 202 395 1860 636 0 0 639 573 70 240 100 78 100 64 2583 2496 2.618 .382 .342 .4 .35 .23 69 307 .54 .95 90 3290 6050 44 53 132 141 0 1577 532 1044 .559 1463 930 1.79 .5 -.84 -1
9 1465 1908 192 340 1273 1568 1485 1817 197 384 1293 1477 0 0 349 648 70 230 99 99 99 94 2841 2770 .812 1.232 1.142 1.28 1.19 .53 86 281 1.31 .97 100 3430 6060 45 55 146 156 0 2791 497 2293 1.801 2657 2160 .555 1.671 .849 .74
10 3374 4385 195 327 3179 4058 3235 3968 203 361 3040 3641 0 0 879 1944 72 210 100 100 100 100 7237 6681 .783 1.277 1.198 1.24 1.22 .39 70 297 1.31 .98 90 3570 6060 45 54 160 169 0 6413 478 5935 1.867 5803 5325 .536 1.752 .901 .809
11 1380 1788 202 359 1178 1429 1407 1707 207 375 1205 1348 0 0 240 624 69 218 100 100 100 100 2607 2553 .824 1.213 1.119 1.25 1.16 .62 69 378 1.3 .97 90 3720 6050 44 53 175 184 0 2615 525 2090 1.774 2497 1972 .564 1.636 .827 .71
12 1791 1996 190 324 1601 1672 1823 1854 197 365 1633 1530 0 0 523 892 66 215 100 94 100 93 3273 3163 .958 1.044 .937 1.03 1.02 .44 69 366 1.13 .98 90 3870 6060 45 54 190 199 0 2919 474 2445 1.527 2712 2238 .655 1.37 .611 .454
13 2667 3566 194 316 2473 3250 2732 3452 199 352 2538 3136 0 0 590 1142 67 199 100 100 100 100 5723 5674 .761 1.314 1.236 1.33 1.27 .42 69 373 1.35 .98 90 4010 6050 44 53 204 213 0 5215 462 4753 1.922 5049 4587 .52 1.807 .943 .854
14 3022 4607 192 326 2830 4281 2863 4011 197 366 2671 3685 0 0 698 2516 66 213 100 100 100 100 7111 6356 .661 1.513 1.38 1.45 1.39 .46 70 379 1.55 .97 90 4180 6050 44 53 221 230 0 6738 477 6261 2.212 5866 5390 .452 2.018 1.146 1.013
15 1589 1851 196 327 1393 1524 1559 1834 199 356 1363 1507 0 0 223 638 65 212 100 98 100 94 2917 2870 .914 1.094 1.106 1.09 1.09 .44 52 335 1.18 .97 80 4320 6060 46 54 236 244 0 2707 478 2229 1.6 2682 2204 .625 1.617 .678 .693
16 6981 5300 196 345 6785 4955 7254 5318 201 377 7058 4973 0 0 1208 1128 68 228 100 100 100 100 11740 12031 1.369 .73 .705 .74 .72 .19 70 371 .76 .99 90 4480 6050 44 53 251 260 0 7752 505 7247 1.068 7778 7273 .936 1.031 .095 .043
17 2252 2123 191 345 2061 1778 2213 1987 201 362 2022 1642 0 0 457 844 70 211 100 99 100 97 3839 3664 1.159 .863 .812 .86 .77 .36 70 326 .96 .97 90 4630 6050 44 53 266 275 0 3105 505 2600 1.262 2906 2402 .793 1.188 .335 .248
18 3567 4428 190 322 3377 4106 3545 4306 199 354 3355 3984 0 0 519 1438 69 210 100 100 100 100 7483 7339 .822 1.216 1.187 1.2 1.22 .35 70 297 1.27 .99 90 4770 6060 45 54 280 289 0 6476 471 6005 1.778 6298 5827 .562 1.737 .83 .796
19 7479 4758 189 324 7290 4434 7511 4465 196 347 7322 4141 0 0 1816 2109 66 191 100 100 100 100 11724 11463 1.644 .608 .566 .59 .58 .22 97 298 .64 .97 110 4910 6050 43 54 293 304 0 6959 474 6485 .89 6530 6056 1.124 .827 -.169 -.274
20 1944 2095 180 335 1764 1760 1933 2125 190 370 1753 1790 0 0 382 706 63 203 100 99 100 99 3524 3543 1.002 .998 1.021 1.01 1 .39 79 325 1.09 .98 100 5060 6060 45 55 309 319 0 3064 490 2574 1.459 3108 2618 .685 1.493 .545 .579

Total number of rows: 41472

Table truncated, full table size 9438 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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