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Sample GSM40688 Query DataSets for GSM40688
Status Public on Jan 27, 2006
Title expression array - AOA1
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AOA1
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55551
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 = 32.43; Parameter Scan Time = 20:53:17; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6677; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; 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 = 32.43; Parameter Scan Time = 20:53:17; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180218; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; 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
1 288 677 69 50 219 627 207 543 76 64 138 493 0 0 184 608 34 115 96 83 90 67 846 631 .349 2.863 3.572 2.183 2.821 3.427 31 125 3.92 .75 60 1920 5300 63 69 57 63 0 329 24 305 1.392 264 240 .718 1.737 .477 .797 .477
2 5407 2076 73 53 5334 2023 849 507 80 64 776 454 0 0 7029 2593 46 58 91 80 89 72 7357 1230 2.637 .379 .585 .39 .378 4.475 121 535 .344 .9 130 2060 5300 59 72 67 80 0 1009 26 984 .184 247 221 5.423 .284 -2.439 -1.814 -2.439
3 613 811 73 54 540 757 520 522 86 65 447 468 0 0 508 888 111 47 73 86 63 81 1297 915 .713 1.402 1.047 1.493 1.011 4.512 38 155 1.98 .65 70 2210 5310 63 70 85 92 0 394 26 368 .682 254 228 1.467 .509 -.553 -.974 -.553
4 542 524 73 53 469 471 441 316 96 65 368 263 0 0 445 451 124 52 77 92 62 80 940 631 .996 1.004 .715 1.226 1.11 5.093 40 139 1.014 .54 60 2360 5300 63 69 101 107 0 255 26 229 .488 154 128 2.048 .347 -1.034 -1.525 -1.034
5 320 256 70 54 250 202 281 117 79 60 211 63 0 0 186 228 40 37 93 70 74 45 452 274 1.238 .808 .299 .527 1.094 6.62 31 193 1.032 .44 70 2500 5300 62 69 114 121 0 124 26 98 .393 57 31 2.545 .145 -1.348 -2.784 -1.348
6 370 211 73 56 297 155 267 183 73 64 194 127 0 0 381 147 12 37 100 73 100 53 452 321 1.916 .522 .655 .587 .661 4.142 26 69 .166 .31 50 2640 5300 63 68 129 134 0 103 27 75 .254 89 62 3.941 .318 -1.978 -1.652 -1.978
7 410 478 71 57 339 421 295 392 174 84 224 335 0 0 364 400 716 113 17 82 4 60 760 559 .805 1.242 1.496 1.328 1.607 4.343 23 73 .222 .46 50 2780 5310 64 69 143 148 0 232 28 205 .604 191 163 1.656 .727 -.728 -.46 -.728
8 291 536 72 51 219 485 272 360 107 62 200 309 0 0 148 696 175 44 64 88 17 88 704 509 .452 2.215 1.545 1.472 1.418 4.489 17 47 8.873 .35 40 2930 5310 65 69 159 163 0 261 25 236 1.077 175 150 .929 .751 .107 -.413 .107
9 1052 1708 72 54 980 1654 899 1366 84 72 827 1312 0 0 818 1270 84 116 88 95 82 89 2634 2139 .593 1.688 1.586 2.008 1.879 3.583 68 262 1.872 .75 90 3090 5300 61 70 172 181 0 830 26 804 .821 664 638 1.219 .771 -.285 -.374 -.285
10 404 157 74 53 330 104 376 89 79 69 302 36 0 0 277 185 75 83 83 33 71 21 434 338 3.173 .315 .119 .195 .144 6.152 56 216 .249 .29 90 3230 5300 61 70 186 195 0 76 26 51 .153 43 18 6.526 .058 -2.706 -4.109 -2.706
11 2251 5509 73 53 2178 5456 2420 5984 80 66 2347 5931 0 0 1499 3396 46 90 89 98 86 95 7634 8278 .399 2.505 2.527 3.447 2.449 3.929 74 299 2.576 .91 100 3380 5300 61 71 201 211 0 2679 26 2653 1.218 2910 2884 .821 1.229 .285 .297 .285
12 5019 14871 72 52 4947 14819 4997 17952 79 67 4925 17900 0 0 4464 12236 42 86 93 97 91 96 19766 22825 .334 2.996 3.635 3.695 3.114 3.245 96 337 3.003 .94 110 3520 5300 60 71 214 225 0 7231 25 7205 1.457 8729 8704 .687 1.767 .543 .821 .543
13 957 1831 72 52 885 1779 795 1414 83 61 723 1362 0 0 654 1551 42 40 98 98 96 98 2664 2085 .497 2.01 1.884 2.067 2.273 3.29 58 190 3.459 .54 80 3670 5300 62 70 231 239 0 890 25 865 .977 688 662 1.023 .916 -.033 -.127 -.033
14 164 428 73 53 91 375 86 312 87 60 13 259 0 0 154 440 91 34 31 95 19 92 466 272 .243 4.121 19.923 6.445 4.766 9.064 63 329 6.581 .34 100 3820 5290 60 70 245 255 0 208 26 182 2.004 152 126 .499 9.687 1.003 3.276 1.003
15 263 686 74 54 189 632 227 603 85 66 153 549 0 0 223 434 89 57 56 98 40 91 821 702 .299 3.344 3.588 4.567 3.578 6.411 62 212 4.78 .45 90 3960 5290 60 69 259 268 0 334 26 307 1.626 293 267 .615 1.745 .701 .803 .701
16 21174 29851 71 55 21103 29796 2817 18065 80 70 2746 18010 0 33 23797 28915 47 83 99 100 98 99 50899 20756 .708 1.412 6.559 1.981 1.433 2.423 127 409 1.299 .96 120 4100 5300 60 72 272 284 0 14514 27 14488 .687 8784 8757 1.457 3.189 -.543 1.673 -.543
17 1629 3042 72 54 1557 2988 1600 2891 79 66 1528 2837 0 0 860 1394 36 68 96 100 96 100 4545 4365 .521 1.919 1.857 2.091 1.825 2.914 56 180 2.219 .72 80 4260 5300 62 70 290 298 0 1479 26 1453 .933 1406 1379 1.072 .903 -.1 -.148 -.1
18 322 2005 71 55 251 1950 240 1933 74 72 169 1878 0 0 276 1156 19 94 79 100 76 98 2201 2047 .129 7.769 11.112 14.788 12.342 6.656 63 239 11.696 .47 90 4400 5290 60 69 303 312 0 975 27 948 3.777 940 913 .265 5.403 1.917 2.434 1.917
19 1919 3716 71 55 1848 3661 1869 4128 79 71 1798 4073 0 0 1192 1942 39 93 95 100 93 98 5509 5871 .505 1.981 2.265 2.464 2.029 3.487 64 248 2.075 .83 90 4540 5290 60 69 317 326 0 1807 27 1780 .963 2007 1980 1.038 1.101 -.054 .139 -.054
20 1212 2961 73 56 1139 2905 1032 2848 81 70 959 2792 0 0 878 1882 41 61 94 100 93 100 4044 3751 .392 2.55 2.911 3.139 2.772 3.036 74 330 2.847 .78 100 4690 5290 60 70 332 342 0 1440 27 1413 1.24 1385 1358 .806 1.416 .31 .501 .31

Total number of rows: 41472

Table truncated, full table size 9247 Kbytes.




Supplementary data files not provided
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