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Sample GSM40708 Query DataSets for GSM40708
Status Public on Jan 27, 2006
Title expression array - GBM10
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM10
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56953
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 = 31.45; Parameter Scan Time = 22:42:33; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13245; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; 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 = 31.45; Parameter Scan Time = 22:42:33; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186850; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; 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
1 324 558 112 59 212 499 325 485 131 79 213 426 0 0 169 427 133 96 65 84 36 73 711 639 .425 2.354 2 2.001 2.185 5.334 83 844 2.645 .45 140 1820 5210 58 72 59 73 0 365 39 326 1.54 317 279 .649 1.308 .623 .388 .623
2 8594 5916 111 61 8483 5855 4191 2825 131 78 4080 2764 0 0 9899 6794 73 60 96 92 94 80 14338 6844 1.449 .69 .677 .617 .702 3.116 105 376 .682 .98 120 1950 5250 63 75 73 85 0 3870 40 3830 .452 1848 1808 2.215 .443 -1.147 -1.174 -1.147
3 708 347 112 56 596 291 642 254 124 61 530 198 0 0 373 236 64 26 97 90 95 85 887 728 2.048 .488 .374 .386 .499 3.962 42 160 .44 .68 70 2100 5250 65 72 90 97 0 227 37 190 .319 166 130 3.131 .244 -1.647 -2.033 -1.647
4 441 163 118 55 323 108 398 105 122 62 280 50 0 0 175 115 55 41 96 62 96 37 431 330 2.991 .334 .179 .247 .233 4.139 29 156 .237 .42 60 2250 5250 66 72 106 112 0 107 36 71 .219 69 33 4.572 .117 -2.193 -3.098 -2.193
5 312 103 111 56 201 47 261 66 133 65 150 10 0 0 185 92 194 69 27 22 8 11 248 160 4.277 .234 .067 .163 .159 5.784 36 144 .079 .15 60 2390 5230 64 70 120 126 0 67 37 31 .153 43 7 6.537 .044 -2.709 -4.519 -2.709
6 332 69 109 56 223 13 345 65 118 59 236 9 0 0 95 26 48 26 90 21 88 4 236 245 17.154 .058 .038 .066 .068 4.082 42 181 -1 -1 70 2540 5240 64 71 134 141 0 45 37 9 .038 43 6 26.222 .025 -4.713 -5.325 -4.713
7 361 92 111 55 250 37 317 56 121 56 206 1 0 0 153 105 49 14 96 31 87 21 287 207 6.757 .148 .005 .129 .082 7.852 32 129 .014 .03 60 2680 5240 65 71 149 155 0 60 36 24 .097 37 1 10.329 .003 -3.369 -8.299 -3.369
8 305 390 109 59 196 331 307 347 123 92 198 288 0 0 156 222 65 128 72 76 61 61 527 486 .592 1.689 1.455 1.763 1.627 6.241 59 293 6.324 .26 100 2840 5250 64 74 163 173 0 255 39 217 1.105 227 188 .905 .952 .144 -.072 .144
9 581 426 106 58 475 368 494 383 125 72 388 325 0 0 351 260 76 64 86 90 80 78 843 713 1.291 .775 .838 .877 .706 5.144 75 232 .586 .49 100 2970 5250 64 74 176 186 0 279 38 241 .507 251 213 1.973 .548 -.98 -.868 -.98
10 652 203 109 59 543 144 546 119 123 85 437 60 0 0 522 329 64 117 94 28 88 15 687 497 3.771 .265 .137 .214 .208 6.424 90 297 -1 -1 110 3120 5240 62 73 190 201 0 133 39 94 .173 78 39 5.764 .09 -2.527 -3.477 -2.527
11 2538 3005 128 64 2410 2941 2469 2927 137 89 2341 2863 0 0 1033 1123 58 117 100 100 100 100 5351 5204 .819 1.22 1.223 1.251 1.222 1.619 85 281 1.226 .85 100 3260 5240 63 73 205 215 0 1966 42 1924 .798 1915 1873 1.253 .8 -.325 -.322 -.325
12 11542 34568 111 62 11431 34506 14351 42720 124 70 14240 42658 0 0 6754 18054 67 50 97 100 96 100 45937 56898 .331 3.019 2.996 3.44 3.014 1.86 92 274 2.96 .98 100 3410 5240 63 73 220 230 0 22614 41 22573 1.975 27946 27906 .506 1.96 .982 .971 .982
13 1674 6886 102 62 1572 6824 1563 7299 110 81 1461 7237 0 0 844 2625 45 81 100 100 100 100 8396 8698 .23 4.341 4.953 4.748 4.447 1.65 83 253 4.436 .89 100 3550 5240 63 73 234 244 0 4505 41 4464 2.84 4775 4734 .352 3.24 1.506 1.696 1.506
14 215 720 104 62 111 658 156 592 123 87 52 530 0 0 133 479 155 123 33 94 13 89 769 582 .169 5.928 10.192 6.49 4.433 4.88 98 278 16.693 .12 110 3700 5240 62 73 248 259 0 471 41 430 3.878 387 347 .258 6.668 1.955 2.737 1.955
15 256 15405 105 63 151 15342 165 16540 127 87 60 16477 0 0 213 4509 165 122 32 100 10 100 15493 16537 .01 101.603 274.617 203.389 188.157 3.867 98 239 122.693 .3 100 3840 5240 63 73 263 273 0 10078 41 10036 66.466 10820 10779 .015 179.647 6.055 7.489 6.055
16 41855 33405 108 65 41747 33340 48019 38233 124 83 47911 38168 4 0 19071 14734 66 87 100 100 100 100 75087 86079 1.252 .799 .797 .821 .791 1.315 91 256 .789 .99 100 3990 5240 63 73 278 288 0 21853 43 21810 .522 25011 24969 1.914 .521 -.937 -.94 -.937
17 2084 5029 100 61 1984 4968 2081 5295 107 86 1981 5234 0 0 1071 2046 38 105 100 100 100 100 6952 7215 .399 2.504 2.642 2.774 2.521 1.839 77 179 2.519 .89 90 4130 5250 64 73 292 301 0 3290 40 3250 1.638 3464 3424 .61 1.728 .712 .789 .712
18 541 2215 100 57 441 2158 512 2287 116 67 412 2230 0 0 284 801 59 36 93 100 89 100 2599 2642 .204 4.893 5.413 5.274 4.772 2.225 76 189 5.395 .76 90 4280 5240 63 72 307 316 0 1449 37 1412 3.201 1496 1459 .312 3.541 1.679 1.824 1.679
19 2150 2715 100 55 2050 2660 2000 2672 110 59 1900 2617 0 0 1170 1259 48 16 100 100 100 100 4710 4517 .771 1.298 1.377 1.388 1.345 1.746 90 278 1.262 .9 110 4430 5240 62 73 321 332 0 1776 36 1740 .849 1748 1712 1.178 .901 -.236 -.15 -.236
20 2578 3830 101 59 2477 3771 2601 3976 108 65 2500 3917 0 0 1375 1704 35 29 100 100 100 100 6248 6417 .657 1.522 1.567 1.677 1.62 1.894 88 269 1.499 .89 100 4570 5240 63 73 336 346 0 2505 39 2467 .996 2601 2562 1.004 1.025 -.006 .036 -.006

Total number of rows: 41472

Table truncated, full table size 9130 Kbytes.




Supplementary data files not provided
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