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Sample GSM40662 Query DataSets for GSM40662
Status Public on Jan 27, 2006
Title expression array - GBM23
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM23
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55563
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 = 30.05; Parameter Scan Time = 18:10:11; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6515; 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 = 30.05; Parameter Scan Time = 18:10:11; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180056; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; 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) mbredel@stanford.edu
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
1 351 273 73 56 278 217 336 181 82 63 263 125 0 0 155 287 35 33 97 87 95 78 495 388 1.281 .781 .475 .609 .488 3.378 41 160 1.691 .35 70 1730 5060 62 69 49 56 0 122 25 97 .349 81 56 2.864 .213 -1.518 -2.234 -1.518
2 4829 10204 74 55 4755 10149 862 2155 93 75 788 2100 0 0 6116 12791 113 61 86 100 67 99 14904 2888 .469 2.134 2.665 2.869 2.236 2.462 115 439 2.137 .98 120 1870 5070 61 73 61 73 0 4565 25 4540 .955 964 939 1.047 1.192 -.067 .254 -.067
3 480 496 75 52 405 444 375 446 83 67 300 394 0 0 287 375 32 52 100 100 93 83 849 694 .912 1.096 1.313 1.035 1.098 2.748 31 58 1.234 .76 50 2020 5060 63 68 79 84 0 222 23 199 .49 200 176 2.039 .587 -1.028 -.767 -1.028
4 409 354 69 54 340 300 372 197 73 80 303 143 0 0 275 470 30 148 84 47 83 32 640 446 1.133 .882 .472 .474 .361 12.617 53 243 4.881 .15 80 2170 5070 63 71 93 101 0 158 24 134 .395 88 64 2.534 .211 -1.341 -2.244 -1.341
5 384 221 67 57 317 164 371 170 72 66 304 113 0 0 213 176 23 39 100 75 88 58 481 417 1.933 .517 .372 .432 .423 7.023 36 137 .233 .21 60 2310 5070 64 70 108 114 0 99 25 73 .231 76 51 4.321 .166 -2.111 -2.588 -2.111
6 334 419 71 59 263 360 313 308 76 89 242 249 0 0 145 407 27 109 96 68 93 53 623 491 .731 1.369 1.029 .848 1.029 3.47 32 148 2.547 .64 60 2460 5070 64 70 123 129 0 187 26 161 .612 138 111 1.633 .46 -.708 -1.119 -.708
7 385 292 71 54 314 238 283 224 78 62 212 170 0 0 298 224 29 27 100 86 93 72 552 382 1.319 .758 .802 .587 .532 3.863 29 143 .582 .5 60 2600 5080 65 71 137 143 0 131 24 106 .339 100 76 2.949 .359 -1.56 -1.479 -1.56
8 274 422 72 55 202 367 164 349 79 64 92 294 0 0 284 318 41 35 52 92 52 84 569 386 .55 1.817 3.196 3.716 3.117 6.123 25 121 1.561 .66 60 2740 5100 67 73 151 157 0 189 25 164 .813 156 132 1.23 1.429 -.299 .516 -.299
9 796 802 71 56 725 746 616 719 86 69 545 663 0 0 540 503 61 44 97 97 95 95 1471 1208 .972 1.029 1.217 1.113 1.039 2.016 70 334 .984 .8 100 2890 5060 61 71 164 174 0 359 25 334 .46 322 297 2.173 .544 -1.119 -.878 -1.119
10 542 366 75 57 467 309 483 309 90 91 408 252 0 0 278 278 56 251 98 50 93 16 776 660 1.511 .662 .618 .554 .561 3.775 74 301 2.847 .21 110 3040 5070 61 72 178 189 0 164 25 138 .296 138 113 3.379 .276 -1.756 -1.856 -1.756
11 2743 5286 76 55 2667 5231 2695 5559 104 103 2619 5504 0 0 1171 2289 123 300 100 100 100 100 7898 8123 .51 1.961 2.102 1.924 1.955 1.605 68 213 2.113 .88 90 3180 5060 61 70 193 202 0 2365 25 2340 .877 2487 2462 1.14 .94 -.189 -.089 -.189
12 6706 22302 71 58 6635 22244 6015 21236 95 95 5944 21178 0 0 5437 17211 107 256 92 98 85 97 28879 27122 .298 3.353 3.563 4.191 3.49 2.14 90 420 3.314 .98 120 3330 5060 60 72 207 219 0 9976 26 9950 1.5 9499 9473 .667 1.594 .585 .672 .585
13 993 4146 71 57 922 4089 1009 4460 91 73 938 4403 0 0 543 1703 91 57 97 100 91 100 5011 5341 .225 4.435 4.694 5.077 4.357 1.879 72 206 4.59 .87 90 3480 5060 61 70 223 232 0 1855 25 1829 1.984 1995 1970 .504 2.1 .988 1.07 .988
14 305 1670 69 56 236 1614 224 1536 80 67 155 1480 0 0 260 941 51 57 80 100 65 100 1850 1635 .146 6.839 9.548 9.95 9.2 3.08 76 236 9.259 .51 90 3620 5060 61 70 237 246 0 747 25 722 3.059 687 662 .327 4.271 1.613 2.095 1.613
15 266 2559 71 58 195 2501 241 2659 84 68 170 2601 0 0 159 975 58 43 77 100 60 100 2696 2771 .078 12.826 15.3 17.372 14.792 2.919 71 291 15.633 .63 100 3770 5060 61 71 252 262 0 1145 26 1119 5.737 1189 1163 .174 6.844 2.52 2.775 2.52
16 24669 27062 71 56 24598 27006 24055 23796 82 70 23984 23740 0 0 21965 23172 47 57 100 100 100 100 51604 47724 .911 1.098 .99 1.175 1.114 1.628 108 396 1.076 .99 120 3920 5060 60 72 266 278 0 12106 25 12080 .491 10645 10620 2.036 .443 -1.026 -1.175 -1.026
17 1936 3565 72 55 1864 3510 1970 3546 78 76 1898 3491 0 0 936 1648 41 70 98 100 98 100 5374 5389 .531 1.883 1.839 2.013 1.894 2.011 67 214 1.953 .9 90 4070 5060 61 70 282 291 0 1595 25 1570 .842 1586 1562 1.187 .823 -.248 -.281 -.248
18 449 3818 72 59 377 3759 356 3892 91 87 284 3833 0 0 348 1435 69 79 84 100 74 100 4136 4117 .1 9.971 13.496 15.764 14.387 2.992 63 231 10.668 .69 90 4210 5060 61 70 296 305 0 1708 26 1681 4.46 1741 1715 .224 6.037 2.157 2.594 2.157
19 2020 4089 72 58 1948 4031 2049 4142 91 79 1977 4084 0 0 1159 2239 62 73 98 100 95 100 5979 6061 .483 2.069 2.066 2.384 2.074 1.839 67 276 2.16 .9 100 4360 5060 61 71 311 321 0 1829 26 1803 .926 1853 1827 1.08 .924 -.111 -.114 -.111
20 1570 3377 72 55 1498 3322 1512 3638 84 71 1440 3583 0 0 928 1568 43 64 96 100 95 100 4820 5023 .451 2.218 2.488 2.432 2.204 1.661 88 316 2.138 .93 110 4500 5060 60 71 324 335 0 1511 25 1486 .992 1627 1603 1.008 1.113 -.012 .154 -.012

Total number of rows: 41472

Table truncated, full table size 9339 Kbytes.




Supplementary data files not provided
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