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Sample GSM40660 Query DataSets for GSM40660
Status Public on Jan 27, 2006
Title expression array - O5
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: O5
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55561
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 = 30.51; Parameter Scan Time = 18:46:28; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6551; 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 = 30.51; Parameter Scan Time = 18:46:28; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180092; 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
1 191 435 83 57 108 378 171 309 93 85 88 252 0 0 85 315 40 118 76 83 58 55 486 340 .286 3.5 2.864 3.492 2.958 2.823 43 229 4.52 .73 80 1790 5210 77 85 63 71 0 211 28 184 1.7 150 122 .588 1.391 .766 .476 .766
2 3865 1630 82 57 3783 1573 644 451 90 81 562 394 0 0 5107 2155 34 79 97 83 95 69 5356 956 2.405 .416 .701 .514 .45 3.026 123 506 .401 .94 130 1940 5200 73 86 75 88 0 792 28 764 .202 219 191 4.951 .341 -2.308 -1.554 -2.308
3 565 485 85 60 480 425 449 332 86 79 364 272 0 0 453 390 19 64 95 85 95 70 905 636 1.129 .885 .747 .772 .797 2.357 40 128 .854 .86 70 2090 5200 76 83 93 100 0 236 29 206 .43 161 132 2.325 .363 -1.217 -1.462 -1.217
4 452 337 82 63 370 274 301 291 86 86 219 228 0 0 340 234 28 82 93 71 89 65 644 447 1.35 .741 1.041 .741 .971 4.379 49 223 .564 .48 80 2240 5200 76 84 108 116 0 164 31 133 .36 141 111 2.78 .506 -1.475 -.983 -1.475
5 222 278 82 66 140 212 186 178 88 91 104 112 0 0 149 278 32 87 76 55 60 39 352 216 .66 1.514 1.077 1.113 1.339 9.076 38 154 13.814 .1 70 2390 5210 77 84 123 130 0 135 32 103 .736 86 54 1.359 .523 -.443 -.935 -.443
6 250 595 83 63 167 532 189 389 99 96 106 326 0 0 184 505 96 111 57 86 26 71 699 432 .314 3.186 3.075 2.498 2.229 3.779 38 155 3.984 .68 70 2530 5210 77 84 137 144 0 289 31 258 1.548 189 158 .646 1.494 .63 .579 .63
7 266 495 82 62 184 433 246 462 107 94 164 400 0 0 152 286 117 156 68 81 28 59 617 564 .425 2.353 2.439 2.53 2.582 3.823 32 164 5.473 .31 70 2670 5210 77 84 151 158 0 240 30 210 1.143 224 194 .875 1.185 .193 .245 .193
8 201 582 83 62 118 520 161 502 88 77 78 440 0 0 144 374 33 48 63 90 53 90 638 518 .227 4.407 5.641 5.704 5.406 4.434 41 163 5.758 .53 70 2820 5190 75 82 166 173 0 283 30 253 2.141 244 214 .467 2.74 1.098 1.454 1.098
9 907 1381 81 60 826 1321 781 1297 90 77 700 1237 0 0 712 722 42 58 97 100 92 100 2147 1937 .625 1.599 1.767 1.988 1.762 2.596 67 317 1.472 .74 100 2970 5200 75 85 180 190 0 671 29 642 .777 630 601 1.287 .858 -.364 -.22 -.364
10 316 291 80 58 236 233 245 274 87 85 165 216 0 0 229 151 34 97 93 77 78 57 469 381 1.013 .987 1.309 1.047 1.252 4.117 75 315 .682 .38 110 3110 5200 74 85 193 204 0 141 28 113 .48 133 105 2.085 .636 -1.06 -.653 -1.06
11 2247 4410 81 57 2166 4353 2294 4676 89 78 2213 4619 0 0 1176 2214 41 93 100 100 98 100 6519 6832 .498 2.01 2.087 2.066 1.99 1.807 76 271 2.062 .93 100 3260 5200 75 85 209 219 0 2142 28 2115 .976 2272 2244 1.024 1.014 -.035 .02 -.035
12 5100 11319 82 58 5018 11261 4714 9954 89 76 4632 9896 0 0 4902 9594 39 65 97 100 95 100 16279 14528 .446 2.244 2.136 2.814 2.424 2.488 110 465 2.184 .93 130 3410 5200 73 86 222 235 0 5499 28 5471 1.09 4836 4807 .917 1.038 .125 .054 .125
13 792 2319 81 60 711 2259 834 2336 89 83 753 2276 0 0 435 1201 40 71 91 100 91 100 2970 3029 .315 3.177 3.023 3.501 3.134 2.34 73 193 3.47 .84 90 3550 5200 75 84 238 247 0 1127 29 1097 1.543 1135 1106 .648 1.468 .626 .554 .626
14 158 1791 80 60 78 1731 107 1786 86 83 27 1726 0 0 108 735 34 74 45 100 40 100 1809 1753 .045 22.192 63.926 33.195 21.323 4.612 85 285 25.178 .48 100 3690 5200 75 85 252 262 0 870 29 841 10.781 868 838 .093 31.055 3.43 4.957 3.43
15 251 4445 82 60 169 4385 191 4611 90 91 109 4551 0 0 246 1869 35 123 65 100 55 100 4554 4660 .039 25.947 41.752 48.419 34.658 4.593 78 260 28.645 .49 100 3840 5200 75 85 267 277 0 2159 29 2130 12.605 2240 2211 .079 20.283 3.656 4.342 3.656
16 25247 23735 81 62 25166 23673 19583 22618 88 95 19502 22556 0 0 22933 20828 34 116 99 100 98 100 48839 42058 1.063 .941 1.157 1.114 .957 2.228 114 402 .92 .97 120 3990 5200 74 86 281 293 0 11530 30 11500 .457 10988 10958 2.188 .562 -1.13 -.832 -1.13
17 1823 5144 82 64 1741 5080 2000 5073 87 96 1918 5009 0 0 751 2082 29 94 98 100 95 100 6821 6927 .343 2.918 2.612 3.141 2.721 1.928 66 214 3.146 .89 90 4130 5190 74 83 296 305 0 2499 31 2468 1.417 2464 2433 .705 1.269 .503 .343 .503
18 381 3198 83 63 298 3135 352 3126 91 90 269 3063 0 0 246 1309 43 76 86 100 77 100 3433 3332 .095 10.52 11.387 15.78 11.728 3.999 72 322 11.76 .69 100 4280 5190 74 84 311 321 0 1554 31 1523 5.111 1519 1488 .196 5.532 2.353 2.468 2.353
19 2266 3704 81 62 2185 3642 2411 3684 87 87 2330 3622 0 0 1010 1620 32 89 100 100 100 100 5827 5952 .6 1.667 1.555 1.752 1.704 1.773 66 223 1.712 .91 90 4420 5200 75 84 325 334 0 1799 30 1769 .81 1790 1760 1.235 .755 -.304 -.405 -.304
20 1260 2276 80 59 1180 2217 1161 1983 86 89 1081 1924 0 0 798 1303 30 117 97 98 97 98 3397 3005 .532 1.879 1.78 2.187 1.699 2.779 77 325 2.074 .77 100 4570 5190 74 84 340 350 0 1106 29 1077 .913 963 935 1.096 .865 -.132 -.21 -.132

Total number of rows: 41472

Table truncated, full table size 9282 Kbytes.




Supplementary data files not provided
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