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Sample GSM40694 Query DataSets for GSM40694
Status Public on Jan 27, 2006
Title expression array - GBM11
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM11
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56913
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 = 31.36; Parameter Scan Time = 20:04:09; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11091; 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 = 31.36; Parameter Scan Time = 20:04:09; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184696; 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) 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
1 367 185 88 52 279 133 367 161 91 69 279 109 0 0 171 118 29 67 97 65 89 41 412 388 2.098 .477 .391 .431 .39 4.618 46 230 .472 .39 80 1840 5220 70 78 52 60 0 100 28 72 .257 87 59 3.884 .211 -1.957 -2.244 -1.957
2 647 1593 91 51 556 1542 447 662 92 61 356 611 0 0 844 2623 27 45 84 100 78 98 2098 967 .361 2.773 1.716 2.914 2.534 3.656 75 252 3.43 .86 90 1980 5220 69 78 65 74 0 860 28 833 1.498 358 330 .668 .927 .583 -.109 .583
3 604 408 91 53 513 355 477 264 97 69 386 211 0 0 506 378 44 113 88 72 80 47 868 597 1.445 .692 .547 .643 .609 4.678 36 191 .528 .47 70 2130 5220 70 77 81 88 0 220 29 192 .374 143 114 2.675 .295 -1.42 -1.76 -1.42
4 597 222 87 51 510 171 547 142 96 59 460 91 0 0 356 231 56 43 93 65 90 50 681 551 2.982 .335 .198 .229 .199 5.619 32 151 .207 .17 60 2280 5210 70 76 97 103 0 120 28 92 .181 77 49 5.521 .107 -2.465 -3.226 -2.465
5 254 129 89 52 165 77 198 78 99 62 109 26 0 0 185 149 63 46 67 33 45 22 242 135 2.143 .467 .239 .36 .303 10.533 53 314 -1 -1 90 2430 5200 67 76 110 119 0 70 28 42 .252 42 14 3.967 .129 -1.988 -2.956 -1.988
6 334 114 88 51 246 63 333 67 91 66 245 16 0 0 142 91 28 71 94 31 88 20 309 261 3.905 .256 .065 .236 .164 5.745 35 171 2.248 .1 70 2570 5220 70 77 125 132 0 62 28 34 .138 36 9 7.229 .035 -2.854 -4.825 -2.854
7 297 310 88 52 209 258 226 207 93 87 138 155 0 0 196 318 35 203 87 38 77 16 467 293 .81 1.234 1.123 1.394 1.049 5.353 31 188 2.346 .41 70 2710 5220 70 77 139 146 0 167 28 139 .667 112 84 1.5 .607 -.585 -.721 -.585
8 364 225 85 52 279 173 343 138 90 72 258 86 0 0 255 193 29 86 96 50 92 35 452 344 1.613 .62 .333 .509 .51 2.979 28 155 .725 .64 60 2850 5210 70 76 154 160 0 122 28 93 .335 75 46 2.986 .18 -1.578 -2.474 -1.578
9 377 308 89 50 288 258 219 166 95 60 130 116 0 0 434 354 44 46 67 72 58 60 546 246 1.116 .896 .892 .815 .968 5.446 43 367 .711 .52 100 3000 5220 69 79 167 177 0 166 27 139 .484 90 63 2.067 .482 -1.047 -1.053 -1.047
10 458 258 91 54 367 204 400 187 95 78 309 133 0 0 318 266 28 132 91 51 85 28 571 442 1.799 .556 .43 .555 .544 11.226 35 132 .302 .22 60 3160 5200 69 75 185 191 0 139 29 110 .3 101 72 3.331 .232 -1.736 -2.105 -1.736
11 2928 3487 87 51 2841 3436 2877 3514 92 63 2790 3463 0 0 1501 1472 44 71 98 100 98 100 6277 6253 .827 1.209 1.241 1.38 1.277 2.793 62 255 1.165 .88 90 3300 5210 68 77 197 206 0 1884 28 1856 .653 1898 1871 1.531 .67 -.614 -.577 -.614
12 8225 27501 89 52 8136 27449 10062 36006 94 64 9973 35954 0 0 6438 18481 38 79 92 100 89 98 35585 45927 .296 3.374 3.605 4.446 3.646 2.898 94 363 3.359 .93 110 3450 5210 67 78 211 222 0 14855 28 14827 1.822 19449 19421 .549 1.947 .866 .962 .866
13 1053 4090 90 50 963 4040 1000 4229 95 63 910 4179 0 0 734 2486 38 66 88 100 87 100 5003 5089 .238 4.195 4.592 5.046 4.443 2.904 80 298 5.017 .74 100 3600 5210 68 78 227 237 0 2209 27 2182 2.266 2284 2257 .441 2.481 1.18 1.311 1.18
14 204 811 87 53 117 758 102 733 90 81 15 680 0 0 367 520 31 144 32 95 27 83 875 695 .154 6.479 45.333 13.031 19.103 6.248 73 293 14.056 .12 100 3740 5210 68 78 241 251 0 438 29 409 3.499 396 367 .286 24.487 1.807 4.614 1.807
15 239 5703 87 54 152 5649 125 6029 90 77 38 5975 0 0 294 3223 29 123 53 100 39 98 5801 6013 .027 37.164 157.237 77.513 73.615 5.636 83 270 47.576 .36 100 3880 5210 68 78 255 265 0 3081 29 3051 20.075 3257 3227 .05 84.932 4.327 6.408 4.327
16 26425 23147 88 53 26337 23094 13849 12491 93 64 13761 12438 1 0 26992 22869 59 49 99 99 98 98 49431 26199 1.14 .877 .904 1.013 .874 2.295 120 448 .855 .97 130 4030 5210 66 79 268 281 0 12503 29 12474 .474 6747 6718 2.111 .488 -1.078 -1.034 -1.078
17 2379 5597 87 52 2292 5545 2221 5692 95 63 2134 5640 0 0 1774 2729 65 54 93 100 93 100 7837 7774 .413 2.419 2.643 3.323 2.815 3.291 76 258 2.323 .83 100 4180 5210 68 78 285 295 0 3023 28 2995 1.307 3075 3046 .765 1.428 .386 .514 .386
18 458 2651 86 54 372 2597 394 2503 107 119 308 2449 0 0 341 1395 238 682 58 94 34 77 2969 2757 .143 6.981 7.951 10.061 9.303 4.04 72 273 6.245 .69 100 4320 5210 68 78 299 309 0 1432 29 1403 3.771 1352 1323 .265 4.295 1.915 2.103 1.915
19 2293 4393 88 53 2205 4340 2039 4433 89 66 1951 4380 0 0 1536 2103 24 49 95 100 94 100 6545 6331 .508 1.968 2.245 2.4 2.092 2.839 71 214 1.961 .8 90 4460 5210 68 77 313 322 0 2373 29 2344 1.063 2395 2366 .941 1.213 .088 .278 .088
20 1884 3710 87 53 1797 3657 1871 3670 97 65 1784 3617 0 0 1126 1941 74 50 97 100 93 100 5454 5401 .491 2.035 2.027 2.39 2.077 2.087 79 303 2.103 .86 100 4610 5210 68 78 328 338 0 2004 29 1975 1.099 1982 1954 .91 1.095 .137 .131 .137

Total number of rows: 41472

Table truncated, full table size 9290 Kbytes.




Supplementary data files not provided
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