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Sample GSM40702 Query DataSets for GSM40702
Status Public on Jan 27, 2006
Title expression array - AOA3
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AOA3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56917
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 = 30.63; Parameter Scan Time = 18:22:58; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 10991; 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 = 30.63; Parameter Scan Time = 18:22:58; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184596; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; 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
1 339 305 84 52 255 253 345 203 99 63 261 151 0 0 192 281 84 53 78 74 68 57 508 412 1.008 .992 .579 .779 .898 4.309 47 231 1.438 .59 80 1640 4960 64 72 40 48 0 145 25 120 .472 97 72 2.119 .275 -1.083 -1.861 -1.083
2 7525 1694 85 52 7440 1642 1414 464 95 62 1329 412 0 0 9258 2135 60 45 93 69 91 67 9082 1741 4.531 .221 .31 .166 .185 4.066 109 530 .206 .9 130 1790 4950 60 73 52 65 0 806 25 781 .105 221 196 9.526 .147 -3.252 -2.762 -3.252
3 774 430 85 53 689 377 604 290 101 65 519 237 0 0 620 350 70 46 85 88 83 78 1066 756 1.828 .547 .457 .548 .494 3.11 42 165 .481 .75 70 1940 4960 64 71 70 77 0 205 25 179 .26 138 113 3.842 .217 -1.942 -2.203 -1.942
4 668 354 83 51 585 303 619 239 96 56 536 188 0 0 430 392 48 23 95 75 92 73 888 724 1.931 .518 .351 .346 .378 5.386 41 183 .559 .55 70 2090 4950 63 70 85 92 0 168 24 144 .246 114 89 4.059 .167 -2.021 -2.583 -2.021
5 337 138 82 52 255 86 266 74 88 59 184 22 0 0 176 157 32 27 97 40 91 27 341 206 2.965 .337 .12 .219 .18 4.628 37 166 .408 .48 70 2230 4960 64 71 99 106 0 66 25 41 .16 35 10 6.234 .057 -2.64 -4.136 -2.64
6 390 303 86 54 304 249 393 256 94 65 307 202 0 0 220 259 47 55 88 68 81 59 553 509 1.221 .819 .658 .702 .649 5.105 44 267 .99 .61 80 2370 4950 63 71 113 121 0 144 26 118 .39 122 96 2.567 .313 -1.36 -1.676 -1.36
7 494 262 81 54 413 208 453 132 93 58 372 78 0 0 267 292 48 22 90 80 90 63 621 450 1.986 .504 .21 .292 .306 5.999 30 65 .442 .33 50 2520 4940 63 68 129 134 0 125 26 99 .24 63 37 4.174 .1 -2.062 -3.326 -2.062
8 342 798 86 56 256 742 255 524 91 75 169 468 0 0 267 614 34 81 78 93 63 82 998 637 .345 2.898 2.769 3.74 3.469 3.815 46 150 3.487 .68 70 2670 4950 63 70 143 150 0 380 27 353 1.379 249 223 .725 1.317 .463 .397 .463
9 896 1021 85 55 811 966 889 955 91 67 804 900 0 0 605 631 38 55 97 98 97 97 1777 1704 .84 1.191 1.119 1.256 1.395 2.294 71 310 1.18 .7 100 2810 4950 62 72 156 166 0 486 26 459 .567 454 428 1.765 .532 -.82 -.909 -.82
10 664 238 85 53 579 185 590 169 94 63 505 116 0 0 465 198 51 46 97 71 94 60 764 621 3.13 .32 .23 .253 .287 4.869 69 212 .198 .47 90 2960 4950 62 71 171 180 0 113 25 88 .152 80 55 6.58 .109 -2.718 -3.194 -2.718
11 3159 5291 82 55 3077 5236 3371 5808 89 77 3289 5753 0 0 1795 2904 53 134 97 98 95 97 8313 9042 .588 1.702 1.749 1.826 1.762 2.327 81 278 1.777 .89 100 3100 4950 62 72 185 195 0 2517 26 2491 .809 2763 2736 1.235 .832 -.305 -.265 -.305
12 9468 28113 84 56 9384 28057 12355 37935 91 74 12271 37879 0 0 7167 21271 52 120 95 99 94 98 37441 50150 .334 2.99 3.087 3.308 3.065 2.615 103 406 3.045 .97 120 3250 4960 62 74 199 211 0 13372 27 13346 1.422 18044 18018 .703 1.468 .508 .554 .508
13 1499 3851 83 54 1416 3797 1395 3891 90 65 1312 3837 0 0 889 1712 44 51 93 100 93 100 5213 5149 .373 2.681 2.925 3.076 2.917 2.246 76 292 2.778 .84 100 3400 4950 62 72 215 225 0 1832 26 1806 1.275 1851 1825 .784 1.391 .351 .476 .351
14 210 2438 82 54 128 2384 125 2435 87 64 43 2381 0 0 211 1126 34 46 57 100 39 100 2512 2424 .054 18.625 55.372 38.482 44.6 4.642 82 303 26.216 .28 100 3540 4950 62 72 229 239 0 1160 26 1134 8.859 1158 1133 .113 26.338 3.147 4.719 3.147
15 312 988 82 55 230 933 240 882 87 72 158 827 0 0 273 586 28 97 77 100 64 98 1163 985 .247 4.057 5.234 6.777 5.39 4.235 62 165 5.321 .5 80 3690 4950 63 71 245 253 0 470 26 444 1.93 420 393 .518 2.49 .948 1.316 .948
16 31387 32232 84 57 31303 32175 34086 35908 97 84 34002 35851 0 6 26997 27107 113 149 99 100 96 99 63478 69853 .973 1.028 1.054 1.266 1.06 1.67 114 406 1.016 .99 120 3830 4950 61 73 257 269 0 15332 27 15304 .489 17080 17053 2.045 .502 -1.032 -.996 -1.032
17 2762 4254 83 56 2679 4198 2575 4205 101 74 2492 4149 0 0 1337 1903 132 89 100 100 100 100 6877 6641 .638 1.567 1.665 1.557 1.607 1.724 71 197 1.641 .84 90 3980 4950 62 71 273 282 0 2023 27 1997 .745 2000 1974 1.342 .792 -.424 -.337 -.424
18 548 4339 82 58 466 4281 432 4200 87 86 350 4142 0 0 767 1768 33 137 85 100 82 100 4747 4492 .109 9.187 11.834 16.372 11.091 3.662 78 275 10.548 .42 100 4120 4950 62 72 287 297 0 2064 28 2036 4.37 1998 1970 .229 5.629 2.128 2.493 2.128
19 2392 4400 81 56 2311 4344 2368 4440 85 70 2287 4384 0 0 1426 2338 29 51 100 100 98 100 6655 6671 .532 1.88 1.917 2.068 1.893 1.894 80 279 1.939 .87 100 4280 4950 62 72 303 313 0 2093 27 2066 .894 2112 2085 1.118 .912 -.161 -.133 -.161
20 2150 4914 81 55 2069 4859 1976 4976 84 71 1895 4921 0 0 1212 2139 30 51 97 100 96 100 6928 6816 .426 2.348 2.597 2.795 2.511 2.648 76 212 2.408 .85 90 4410 4950 62 71 316 325 0 2337 26 2311 1.117 2367 2341 .895 1.235 .16 .305 .16

Total number of rows: 41472

Table truncated, full table size 9343 Kbytes.




Supplementary data files not provided
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