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Sample GSM40695 Query DataSets for GSM40695
Status Public on Jan 27, 2006
Title expression array - GBM9
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM9
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56914
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 20:53:31; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11140; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 20:53:31; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184745; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
 
Submission date Feb 01, 2005
Last update date Mar 22, 2006
Contact name Markus Bredel
E-mail(s) [email protected]
Phone 650-498-6012
Organization name Stanford University School of Medicine
Street address
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1833
Series (1)
GSE2223 Gene expression profiling in human glial brain tumors

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 417 1716 86 52 331 1664 382 1389 107 71 296 1337 0 0 264 1183 77 76 93 100 82 100 1995 1633 .199 5.027 4.517 5.08 5.647 2.458 45 158 8.997 .51 70 1860 5460 62 69 50 57 0 1126 34 1092 3.299 912 877 .303 2.964 1.722 1.568 1.722
2 5471 20189 85 51 5386 20138 748 2538 98 62 663 2487 0 15 7688 26201 61 59 87 100 77 99 25524 3150 .267 3.739 3.751 5.422 4.087 2.96 132 449 3.578 .97 120 2010 5460 60 72 63 75 0 13249 33 13216 2.454 1666 1632 .408 2.462 1.295 1.3 1.295
3 738 734 83 51 655 683 639 536 98 64 556 485 0 0 471 712 77 56 86 91 83 88 1338 1041 .959 1.043 .872 1.015 .951 4.003 36 229 1.32 .77 80 2160 5470 63 71 80 88 0 482 33 448 .684 352 318 1.461 .572 -.547 -.805 -.547
4 637 293 86 52 551 241 483 228 95 66 397 176 0 0 424 230 55 75 97 78 89 57 792 573 2.286 .437 .443 .373 .492 4.14 38 180 .255 .41 70 2300 5470 63 70 94 101 0 192 34 158 .287 150 116 3.484 .291 -1.801 -1.781 -1.801
5 356 124 84 52 272 72 298 69 100 62 214 17 0 0 219 120 61 55 91 30 80 25 344 231 3.778 .265 .079 .156 .137 7.512 36 144 .102 .16 60 2450 5460 63 69 110 116 0 81 34 47 .174 45 11 5.757 .052 -2.525 -4.262 -2.525
6 385 71 86 51 299 20 382 61 91 60 296 10 0 0 167 38 33 37 97 14 94 2 319 306 14.95 .067 .034 .053 .063 4.668 35 179 .084 .33 70 2590 5470 63 70 123 130 0 47 33 13 .044 40 7 22.781 .022 -4.51 -5.495 -4.51
7 397 216 84 51 313 165 321 143 98 56 237 92 0 0 219 206 67 27 96 71 82 64 478 329 1.897 .527 .388 .31 .382 5.766 28 152 .476 .36 60 2730 5470 64 70 138 144 0 142 33 108 .346 94 60 2.891 .255 -1.531 -1.973 -1.531
8 364 403 87 52 277 351 370 277 100 58 283 225 0 0 165 483 66 38 92 96 76 72 628 508 .789 1.267 .795 .962 .948 3.968 25 147 4.801 .32 60 2890 5470 64 70 154 160 0 264 34 230 .832 182 148 1.203 .522 -.266 -.939 -.266
9 964 860 83 53 881 807 825 731 93 82 742 678 0 0 664 610 48 207 100 80 96 71 1688 1420 1.092 .916 .914 .832 .911 3.651 63 262 .976 .57 90 3030 5460 61 70 166 175 0 564 35 530 .601 480 445 1.664 .6 -.734 -.738 -.734
10 712 351 84 53 628 298 582 287 90 77 498 234 0 0 635 315 34 212 95 53 85 23 926 732 2.107 .475 .47 .502 .509 4.597 63 238 .269 .42 90 3180 5460 61 70 181 190 0 230 35 196 .311 188 154 3.211 .308 -1.683 -1.697 -1.683
11 3498 2219 83 53 3415 2166 3454 2113 100 65 3371 2060 0 0 1613 1199 119 60 100 100 100 100 5581 5431 1.577 .634 .611 .614 .626 1.863 64 228 .622 .86 90 3320 5460 61 70 195 204 0 1456 35 1421 .416 1387 1352 2.402 .401 -1.265 -1.318 -1.265
12 8539 25158 84 53 8455 25105 11175 29208 94 68 11091 29155 0 0 6900 20008 91 74 85 99 83 97 33560 40246 .337 2.969 2.629 4.117 3.144 3.011 102 401 3.009 .97 120 3470 5460 60 72 209 221 0 16510 35 16475 1.949 19168 19133 .513 1.725 .962 .787 .962
13 1135 5674 85 54 1050 5620 1105 6368 92 68 1020 6314 0 0 916 3426 39 61 84 98 78 98 6670 7334 .187 5.352 6.19 7.176 6.905 2.621 85 316 5.57 .81 110 3620 5460 60 71 224 235 0 3724 35 3688 3.513 4179 4144 .285 4.062 1.813 2.022 1.813
14 185 398 86 53 99 345 126 296 93 60 40 243 0 0 127 424 42 37 49 82 31 76 444 283 .287 3.485 6.075 3.967 3.984 7.715 69 287 21.935 .13 100 3760 5460 61 71 239 249 0 261 35 226 2.287 194 159 .437 3.987 1.193 1.995 1.193
15 284 4714 86 52 198 4662 188 4952 94 60 102 4900 0 0 262 2144 50 47 64 100 50 100 4860 5002 .042 23.545 48.039 41.475 35.534 3.618 75 277 24.622 .58 100 3900 5460 61 71 253 263 0 3094 34 3059 15.452 3250 3216 .065 31.526 3.95 4.978 3.95
16 27455 19746 86 56 27369 19690 21368 14464 97 73 21282 14408 0 0 25713 18183 59 83 98 100 96 98 47059 35690 1.39 .719 .677 .905 .738 2.306 117 398 .709 .98 120 4050 5460 60 72 267 279 0 12958 37 12922 .472 9492 9455 2.118 .444 -1.083 -1.17 -1.083
17 2009 4680 89 58 1920 4622 1988 4429 111 85 1899 4371 0 0 1183 2196 96 95 94 100 94 100 6542 6270 .415 2.407 2.302 2.813 2.585 2.129 70 204 2.506 .84 90 4200 5450 60 69 283 292 0 3071 38 3033 1.58 2907 2868 .633 1.511 .66 .595 .66
18 447 1044 86 55 361 989 338 866 108 79 252 811 0 0 418 648 91 90 73 97 59 96 1350 1063 .365 2.74 3.218 3.644 3.354 4.29 76 280 3.192 .53 100 4340 5460 61 71 297 307 0 685 36 649 1.798 568 532 .556 2.112 .846 1.079 .846
19 2493 3976 82 53 2411 3923 2309 4060 90 58 2227 4007 0 0 1559 1678 48 33 98 100 95 100 6334 6234 .615 1.627 1.799 1.976 1.838 2.456 68 232 1.564 .82 90 4490 5450 60 69 312 321 0 2609 35 2574 1.068 2664 2630 .937 1.181 .095 .24 .095
20 1707 2222 80 51 1627 2171 1493 2187 86 56 1413 2136 0 0 1239 1203 38 32 97 100 96 98 3798 3549 .749 1.334 1.512 1.593 1.256 2.766 78 293 1.223 .73 100 4630 5460 61 71 326 336 0 1458 33 1425 .876 1435 1402 1.142 .992 -.192 -.012 -.192

Total number of rows: 41472

Table truncated, full table size 9193 Kbytes.




Supplementary data files not provided
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