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Sample GSM40684 Query DataSets for GSM40684
Status Public on Jan 27, 2006
Title expression array - GBM14
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM14
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56929
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 = 31.42; Parameter Scan Time = 19:35:08; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12024; 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 = 31.42; Parameter Scan Time = 19:35:08; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185629; 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
1 540 622 134 54 406 568 512 546 145 61 378 492 0 0 240 324 53 40 100 100 92 97 974 870 .715 1.399 1.302 1.407 1.335 2.303 38 166 1.653 .71 70 1810 5680 64 71 57 64 0 383 33 350 .861 336 303 1.161 .801 -.215 -.32 -.215
2 6314 3376 136 55 6178 3321 1958 1352 148 68 1822 1297 0 0 7024 3711 64 69 97 93 95 88 9499 3119 1.86 .538 .712 .522 .551 2.567 108 528 .519 .96 130 1950 5680 61 74 68 81 0 2078 34 2044 .331 832 798 3.022 .438 -1.595 -1.19 -1.595
3 1107 859 137 56 970 803 819 600 148 63 682 544 0 0 922 781 55 29 89 97 76 89 1773 1226 1.208 .828 .798 1.025 .69 4.931 39 149 .806 .79 70 2100 5690 65 72 86 93 0 529 34 494 .51 369 335 1.962 .491 -.972 -1.026 -.972
4 990 370 135 58 855 312 907 288 139 63 772 230 0 0 674 286 34 28 100 80 94 77 1167 1002 2.74 .365 .298 .37 .388 3.257 35 181 .325 .76 70 2250 5690 65 72 101 108 0 228 36 192 .225 177 142 4.451 .183 -2.154 -2.447 -2.154
5 495 265 133 56 362 209 400 151 134 71 267 95 0 0 337 312 28 68 96 57 90 42 571 362 1.732 .577 .356 .407 .464 6.057 33 151 .45 .28 60 2400 5680 65 71 117 123 0 163 34 129 .355 93 58 2.814 .219 -1.492 -2.191 -1.492
6 614 261 123 58 491 203 443 247 123 72 320 189 0 0 422 227 23 58 100 65 96 59 694 509 2.419 .413 .591 .401 .544 3.949 32 188 .33 .44 70 2540 5680 64 71 130 137 0 161 36 125 .255 152 116 3.929 .364 -1.974 -1.46 -1.974
7 527 428 135 58 392 370 426 267 140 76 291 209 0 0 297 342 48 62 96 96 92 74 762 500 1.059 .944 .718 .847 .985 3.349 27 149 .942 .49 60 2690 5690 66 72 146 152 0 263 36 228 .581 164 129 1.721 .442 -.783 -1.177 -.783
8 544 766 135 66 409 700 537 669 144 80 402 603 0 0 164 417 41 68 95 100 95 100 1109 1005 .584 1.711 1.5 1.608 1.793 2.136 21 75 2.25 .81 50 2830 5690 66 71 160 165 0 472 41 431 1.054 412 371 .949 .923 .075 -.115 .075
9 1140 1227 128 60 1012 1167 971 1089 134 77 843 1029 0 0 654 759 40 77 100 98 98 95 2179 1872 .867 1.153 1.221 1.143 1.2 2.817 62 272 1.232 .69 90 2980 5670 62 71 173 182 0 755 37 718 .71 670 633 1.409 .751 -.494 -.412 -.494
10 508 450 130 73 378 377 424 334 150 145 294 261 0 0 340 413 103 200 81 59 66 31 755 555 1.003 .997 .888 .891 .805 5.527 72 266 1.484 .33 100 3130 5680 63 73 188 198 0 277 45 232 .614 206 161 1.629 .547 -.704 -.872 -.704
11 3743 5131 133 60 3610 5071 3624 5254 149 101 3491 5194 0 0 2284 2496 70 160 97 100 94 100 8681 8685 .712 1.405 1.488 1.675 1.32 2.207 74 262 1.349 .87 100 3270 5680 63 73 202 212 0 3159 37 3122 .865 3234 3197 1.156 .916 -.21 -.127 -.21
12 7188 16582 126 57 7062 16525 9277 18393 140 70 9151 18336 0 0 4949 11428 66 57 97 100 97 100 23587 27487 .427 2.34 2.004 2.739 2.349 1.996 84 304 2.411 .95 100 3410 5670 62 72 216 226 0 10208 35 10173 1.441 11323 11288 .694 1.234 .527 .303 .527
13 1591 5392 129 60 1462 5332 1653 5995 140 73 1524 5935 0 0 936 2386 50 51 92 100 92 100 6794 7459 .274 3.647 3.894 4.318 3.902 2.274 66 233 3.739 .86 90 3560 5670 62 71 231 240 0 3319 37 3282 2.245 3691 3654 .445 2.397 1.167 1.261 1.167
14 336 2307 132 58 204 2249 189 2083 139 67 57 2025 0 0 336 1238 38 44 53 100 47 100 2453 2082 .091 11.025 35.526 14.033 10.64 5.045 80 308 13.635 .43 100 3700 5670 62 72 245 255 0 1420 36 1385 6.787 1282 1247 .147 21.87 2.763 4.451 2.763
15 543 10133 133 60 410 10073 402 11134 141 68 269 11074 0 0 468 4262 44 38 73 100 67 100 10483 11343 .041 24.568 41.167 46.79 43.354 3.756 78 264 25.135 .64 100 3850 5680 63 73 260 270 0 6238 37 6201 15.125 6854 6817 .066 25.343 3.919 4.664 3.919
16 35172 29835 134 61 35038 29774 42313 28782 146 79 42179 28721 22 0 28506 23853 59 81 100 100 100 100 64812 70900 1.177 .85 .681 .973 .854 1.875 98 300 .84 .98 110 3990 5680 62 73 273 284 0 18367 38 18329 .523 17719 17681 1.912 .419 -.935 -1.254 -.935
17 2222 6082 131 62 2091 6020 2073 6455 139 82 1942 6393 0 0 1363 2923 42 90 97 100 97 100 8111 8335 .347 2.879 3.292 3.176 2.873 2.207 68 224 3.029 .83 90 4140 5670 62 71 289 298 0 3744 38 3706 1.772 3974 3936 .564 2.027 .826 1.019 .826
18 612 3091 127 58 485 3033 546 2952 133 64 419 2894 0 0 392 1492 38 39 85 100 84 100 3518 3313 .16 6.254 6.907 8.114 5.864 3.114 57 194 7.465 .68 80 4290 5670 63 71 305 313 0 1903 36 1867 3.85 1817 1782 .26 4.252 1.945 2.088 1.945
19 3190 3324 127 58 3063 3266 3210 3796 139 69 3083 3738 0 0 1793 1589 72 47 100 100 98 100 6329 6821 .938 1.066 1.212 1.149 1.083 2.088 74 285 1.011 .87 100 4430 5670 62 72 318 328 0 2046 36 2011 .656 2337 2301 1.523 .746 -.607 -.422 -.607
20 2413 3359 132 57 2281 3302 2272 3585 136 63 2140 3528 0 0 1458 1986 34 34 100 100 100 100 5583 5668 .691 1.448 1.649 1.468 1.546 2.207 75 289 1.517 .83 100 4570 5670 62 72 332 342 0 2068 35 2033 .891 2207 2172 1.122 1.015 -.166 .021 -.166

Total number of rows: 41472

Table truncated, full table size 9340 Kbytes.




Supplementary data files not provided
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