NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM40712 Query DataSets for GSM40712
Status Public on Jan 27, 2006
Title expression array - GBM8
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM8
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56955
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 = 30.54; Parameter Scan Time = 20:26:43; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13110; 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 = 30.54; Parameter Scan Time = 20:26:43; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186715; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; 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
1 315 113 113 54 202 59 314 71 116 62 201 17 0 0 63 119 30 41 100 28 100 21 261 218 3.424 .292 .085 .138 .154 4.351 42 175 .446 .35 70 1850 5790 67 74 57 64 0 67 32 35 .174 42 10 5.738 .05 -2.521 -4.309 -2.521
2 5065 16229 108 53 4957 16176 3743 12174 112 56 3635 12121 0 0 4902 16023 31 18 93 100 87 100 21133 15756 .306 3.263 3.335 3.813 3.498 1.875 83 361 3.332 .98 100 1990 5790 66 76 70 80 0 9683 32 9651 1.947 7264 7232 .514 1.99 .961 .992 .961
3 488 313 109 55 379 258 429 208 114 57 320 153 0 0 224 239 28 16 100 96 100 90 637 473 1.469 .681 .478 .517 .599 2.698 33 145 .791 .66 60 2140 5790 68 74 87 93 0 187 33 154 .406 124 91 2.462 .285 -1.3 -1.81 -1.3
4 367 198 110 54 257 144 353 79 114 59 243 25 0 0 131 259 32 25 100 48 97 45 401 268 1.785 .56 .103 .247 .225 7.837 35 198 1.429 .39 70 2290 5790 67 74 101 108 0 118 32 86 .334 47 15 2.991 .061 -1.581 -4.026 -1.581
5 295 114 109 54 186 60 230 69 110 56 121 15 0 0 155 98 25 18 97 44 92 42 246 136 3.1 .323 .124 .325 .425 6.442 38 251 .144 .2 80 2440 5790 67 75 116 124 0 68 32 36 .192 41 9 5.196 .074 -2.377 -3.757 -2.377
6 334 101 109 60 225 41 325 73 112 65 216 13 0 0 106 109 24 39 100 23 97 7 266 229 5.488 .182 .06 .136 .138 5.019 39 134 .118 .14 60 2580 5790 68 74 131 137 0 60 36 24 .109 44 8 9.198 .036 -3.201 -4.8 -3.201
7 266 92 106 57 160 35 240 63 109 62 134 6 0 0 143 75 25 44 97 19 82 9 195 140 4.571 .219 .045 .193 .175 4.382 41 175 .252 .49 70 2720 5790 67 74 144 151 0 55 34 21 .131 38 4 7.662 .027 -2.938 -5.226 -2.938
8 352 232 108 53 244 179 317 123 113 63 209 70 0 0 187 256 27 59 93 57 93 36 423 279 1.363 .734 .335 .348 .452 7.174 33 137 1.753 .25 60 2870 5780 67 73 160 166 0 138 32 107 .438 73 42 2.285 .2 -1.192 -2.323 -1.192
9 531 396 103 55 428 341 420 342 106 63 317 287 0 0 405 273 22 58 93 87 90 83 769 604 1.255 .797 .905 .889 .954 4.331 62 239 .556 .51 90 3010 5790 66 75 172 181 0 236 33 203 .475 204 171 2.104 .54 -1.073 -.888 -1.073
10 452 214 101 56 351 158 343 136 104 64 242 80 0 0 301 199 26 53 98 62 92 44 509 322 2.222 .45 .331 .355 .388 5.24 77 299 .312 .41 110 3150 5790 65 76 185 196 0 128 33 94 .269 81 48 3.723 .197 -1.897 -2.342 -1.897
11 1619 2259 103 56 1516 2203 1401 2163 106 59 1298 2107 0 0 1029 1004 31 18 97 100 95 100 3719 3405 .688 1.453 1.623 1.74 1.647 2.404 83 285 1.351 .82 100 3300 5790 66 76 201 211 0 1348 33 1314 .867 1291 1257 1.153 .969 -.206 -.046 -.206
12 8907 27625 102 54 8805 27571 10099 30802 108 61 9997 30748 0 0 4328 12253 35 39 100 100 98 100 36376 40745 .319 3.131 3.076 3.463 3.125 1.778 79 320 3.109 .98 100 3450 5790 66 76 216 226 0 16482 32 16450 1.868 18378 18346 .535 1.835 .902 .876 .902
13 1231 3537 106 55 1125 3482 1096 3525 110 58 990 3470 0 0 752 1288 34 22 100 100 100 100 4607 4460 .323 3.095 3.505 3.652 3.149 2.153 66 239 3.253 .77 90 3600 5780 65 74 231 240 0 2110 33 2078 1.847 2103 2070 .542 2.091 .885 1.064 .885
14 179 795 105 56 74 739 127 702 110 61 22 646 0 0 123 369 33 30 41 100 29 100 813 668 .1 9.986 29.364 12.231 16.182 4.103 87 267 15.665 .3 100 3740 5790 66 76 245 255 0 474 33 441 5.958 419 385 .168 17.52 2.575 4.131 2.575
15 170 5976 100 54 70 5922 128 6211 110 59 28 6157 0 0 126 1942 41 22 38 100 25 100 5992 6185 .012 84.6 219.893 139.091 136.725 4.3 94 234 115.865 .31 100 3880 5790 66 76 259 269 0 3566 32 3533 50.476 3706 3674 .02 131.198 5.658 7.036 5.658
16 27296 20008 106 56 27190 19952 30603 21889 111 59 30497 21833 0 0 16290 11601 34 19 98 100 98 100 47142 52330 1.363 .734 .716 .839 .703 2.298 90 274 .719 .97 100 4030 5790 66 76 274 284 0 11938 33 11904 .438 13060 13027 2.284 .427 -1.192 -1.227 -1.192
17 1611 3012 106 57 1505 2955 1588 2832 118 62 1482 2775 0 0 782 1318 68 24 97 100 97 100 4460 4257 .509 1.963 1.872 2.08 1.997 2.177 71 215 2.105 .83 90 4180 5780 65 74 289 298 0 1797 34 1763 1.171 1690 1656 .854 1.117 .228 .16 .228
18 419 2673 102 56 317 2617 330 2374 111 59 228 2318 0 0 358 1045 67 19 79 100 70 100 2934 2546 .121 8.256 10.167 11.202 9.383 2.583 74 204 8.326 .63 90 4320 5780 65 74 303 312 0 1595 33 1561 4.926 1416 1383 .203 6.066 2.3 2.601 2.3
19 1459 2375 99 55 1360 2320 1368 2198 104 60 1269 2143 0 0 905 1241 30 27 98 100 98 100 3680 3412 .586 1.706 1.689 2.016 1.921 2.206 87 258 1.727 .82 100 4470 5780 65 75 318 328 0 1417 33 1384 1.018 1311 1279 .983 1.008 .025 .011 .025
20 1748 3085 99 56 1649 3029 1652 3206 107 62 1553 3150 0 0 904 1326 43 31 100 100 100 100 4678 4703 .544 1.837 2.028 1.938 1.875 1.999 83 267 1.859 .88 100 4610 5790 66 76 332 342 0 1841 33 1807 1.096 1913 1879 .912 1.21 .132 .275 .132

Total number of rows: 41472

Table truncated, full table size 9178 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap