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Sample GSM40706 Query DataSets for GSM40706
Status Public on Jan 27, 2006
Title expression array - AOA7
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AOA7
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56951
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 = 31.27; Parameter Scan Time = 21:41:32; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13184; 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 = 31.27; Parameter Scan Time = 21:41:32; Parameter PMT Volts = 770; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186789; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; 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
1 323 164 81 93 242 71 320 120 86 105 239 27 0 0 78 97 24 61 100 42 100 20 313 266 3.408 .293 .113 .215 .307 4.824 40 195 .257 .18 70 1810 5290 57 64 81 88 0 94 53 41 .168 69 15 5.95 .065 -2.573 -3.95 -2.573
2 9912 1116 83 86 9829 1030 10229 894 88 99 10146 808 0 0 5160 754 30 64 100 94 100 94 10859 10954 9.543 .105 .08 .091 .097 2.446 55 240 .087 .73 80 1960 5290 57 65 96 104 0 639 49 590 .06 512 463 16.657 .046 -4.058 -4.454 -4.058
3 441 248 79 92 362 156 416 180 85 132 337 88 0 0 261 200 45 266 93 17 88 6 518 425 2.321 .431 .261 .393 .396 5.112 45 152 .303 .28 70 2110 5300 58 65 111 118 0 142 53 89 .247 103 50 4.05 .15 -2.018 -2.741 -2.018
4 318 187 81 95 237 92 284 140 88 107 203 45 0 0 166 164 45 62 94 36 92 15 329 248 2.576 .388 .222 .328 .329 5.513 38 167 .118 .08 70 2250 5300 58 65 125 132 0 107 54 53 .222 80 26 4.497 .127 -2.169 -2.977 -2.169
5 218 371 83 92 135 279 193 215 87 113 110 123 0 0 87 508 26 113 97 54 85 35 414 233 .484 2.067 1.118 1.232 1.697 6.458 42 248 17.37 .2 80 2400 5290 57 65 140 148 0 213 53 160 1.184 123 70 .845 .641 .244 -.642 .244
6 322 158 82 90 240 68 317 115 89 102 235 25 0 0 133 113 44 64 97 24 94 18 308 260 3.529 .283 .106 .207 .14 5.133 37 137 .14 .13 60 2550 5290 58 64 156 162 0 91 52 39 .162 66 14 6.161 .061 -2.623 -4.036 -2.623
7 282 153 82 95 200 58 253 123 86 123 171 28 0 0 95 125 28 132 100 10 100 6 258 199 3.448 .29 .164 .269 .272 4.236 29 150 .113 .06 60 2690 5300 59 65 170 176 0 88 54 33 .166 70 16 6.019 .094 -2.59 -3.414 -2.59
8 340 128 92 97 248 31 342 126 101 103 250 29 0 0 56 50 38 46 100 27 100 3 279 279 8 .125 .116 .122 .149 2.527 29 64 .116 .14 50 2840 5280 57 62 185 190 0 73 56 18 .072 72 17 13.964 .066 -3.804 -3.911 -3.804
9 417 410 85 96 332 314 352 330 92 129 267 234 0 0 236 285 40 148 96 61 91 45 646 501 1.057 .946 .876 .949 1.024 4.578 62 224 1.586 .32 90 2990 5290 56 65 198 207 0 235 55 180 .542 189 134 1.846 .502 -.884 -.994 -.884
10 494 437 82 96 412 341 461 150 86 132 379 54 0 0 281 1109 31 146 97 32 95 22 753 433 1.208 .828 .142 .322 .232 7.576 68 303 28.366 .08 110 3120 5290 55 66 210 221 0 250 55 195 .474 86 31 2.109 .082 -1.077 -3.615 -1.077
11 1695 2981 81 92 1614 2889 1614 2832 84 109 1533 2740 0 0 778 1471 27 89 100 100 98 100 4503 4273 .559 1.79 1.787 1.815 1.764 2.355 83 275 2.098 .78 100 3270 5290 56 66 226 236 0 1708 53 1655 1.025 1622 1570 .975 1.024 .036 .034 .036
12 8259 18759 79 93 8180 18666 8745 18906 82 121 8666 18813 0 0 3823 8429 25 203 100 100 100 100 26846 27479 .438 2.282 2.171 2.359 2.302 1.457 84 294 2.339 .95 100 3420 5300 57 67 241 251 0 10747 53 10694 1.307 10831 10778 .765 1.244 .387 .315 .387
13 1026 1773 79 90 947 1683 994 1581 84 124 915 1491 0 0 505 1002 25 231 100 97 98 91 2630 2406 .563 1.777 1.63 1.757 1.7 2.664 73 223 2.15 .77 90 3560 5290 56 65 255 264 0 1016 52 964 1.018 906 854 .982 .934 .026 -.099 .026
14 193 672 81 94 112 578 119 640 87 106 38 546 0 0 171 436 35 60 53 92 40 90 690 584 .194 5.161 14.368 8.628 9.943 8.165 64 330 14.833 .19 110 3710 5290 55 66 269 280 0 385 54 331 2.957 367 313 .338 8.232 1.564 3.041 1.564
15 267 617 78 101 189 516 213 563 84 127 135 462 0 0 185 315 28 143 77 90 66 75 705 597 .366 2.73 3.422 4.131 4.414 5.087 62 261 4.976 .41 100 3850 5290 56 66 284 294 0 353 58 296 1.564 323 265 .639 1.961 .645 .971 .645
16 25959 32835 80 95 25879 32740 27805 33617 89 124 27725 33522 0 0 10550 14280 62 141 100 100 100 100 58619 61247 .79 1.265 1.209 1.251 1.251 1.322 84 289 1.287 .98 100 4000 5290 56 66 299 309 0 18811 54 18757 .725 19259 19205 1.38 .693 -.464 -.53 -.464
17 1266 1147 81 88 1185 1059 1167 1037 85 101 1086 949 0 0 495 641 26 62 100 100 98 98 2244 2035 1.119 .894 .874 .819 .861 2.626 64 202 .972 .7 90 4150 5290 56 65 314 323 0 657 50 607 .512 594 544 1.953 .501 -.966 -.998 -.966
18 344 1735 83 95 261 1640 277 1445 91 120 194 1350 0 0 243 1145 52 114 82 97 67 93 1901 1544 .159 6.284 6.959 7.044 7.5 3.854 81 268 10.903 .35 100 4300 5280 55 65 329 339 0 994 54 940 3.6 828 773 .278 3.987 1.848 1.995 1.848
19 1312 949 81 94 1231 855 1172 826 94 113 1091 732 0 0 740 666 70 82 100 96 97 91 2086 1823 1.44 .695 .671 .614 .654 2.507 84 265 .703 .71 100 4440 5290 56 66 343 353 0 544 54 490 .398 473 419 2.513 .384 -1.329 -1.379 -1.329
20 1138 1628 80 96 1058 1532 1224 1260 90 114 1144 1164 0 0 611 1049 54 80 95 98 95 98 2590 2308 .691 1.448 1.017 1.589 1.354 3.111 88 301 1.767 .74 100 4580 5290 56 66 357 367 0 933 55 878 .83 722 667 1.205 .583 -.27 -.779 -.27

Total number of rows: 41472

Table truncated, full table size 9192 Kbytes.




Supplementary data files not provided
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