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Sample GSM40664 Query DataSets for GSM40664
Status Public on Jan 27, 2006
Title expression array - AOA2
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AOA2
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55564
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 = 31.48; Parameter Scan Time = 20:12:13; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6637; 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 = 31.48; Parameter Scan Time = 20:12:13; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180178; 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
1 341 409 75 56 266 353 314 367 85 73 239 311 0 0 187 238 43 51 97 89 84 87 619 550 .754 1.327 1.301 1.446 1.333 3.457 39 163 1.559 .49 70 1710 5160 60 67 55 62 0 247 34 213 .801 221 188 1.249 .785 -.32 -.349 -.32
2 6585 538 72 57 6513 481 1633 200 83 88 1561 143 0 0 7608 627 58 108 100 55 100 45 6994 1704 13.541 .074 .092 .062 .067 3.204 114 461 .071 .89 120 1860 5160 58 70 68 80 0 325 34 290 .045 121 86 22.438 .055 -4.488 -4.177 -4.488
3 835 702 73 54 762 648 744 682 81 80 671 628 0 0 532 485 31 102 94 84 94 76 1410 1299 1.176 .85 .936 .77 .786 2.599 38 150 .85 .8 70 2000 5170 61 68 84 91 0 424 33 391 .513 412 379 1.949 .565 -.962 -.824 -.962
4 403 258 70 54 333 204 374 130 76 69 304 76 0 0 244 319 29 69 94 52 88 41 537 380 1.632 .613 .25 .32 .285 7.211 36 191 1.411 .24 70 2160 5160 60 67 100 107 0 156 33 123 .37 78 46 2.705 .151 -1.436 -2.729 -1.436
5 276 104 71 63 205 41 249 89 78 102 178 26 0 0 111 60 39 121 97 8 91 0 246 204 5 .2 .146 .248 .414 3.701 35 198 .078 .07 70 2300 5150 59 66 114 121 0 63 38 25 .121 54 16 8.285 .088 -3.051 -3.504 -3.051
6 353 104 73 68 280 36 322 76 82 85 249 8 0 0 158 74 32 56 96 23 96 23 316 257 7.778 .129 .032 .21 .189 7.206 26 66 .062 .13 50 2440 5160 61 66 129 134 0 63 41 22 .078 46 5 12.888 .019 -3.688 -5.689 -3.688
7 384 450 74 58 310 392 287 300 83 65 213 242 0 0 235 321 28 31 96 92 96 88 702 455 .791 1.265 1.136 1.093 1.264 3.198 27 159 1.476 .7 60 2600 5160 61 67 145 151 0 272 35 237 .763 181 146 1.31 .686 -.39 -.544 -.39
8 344 1205 72 60 272 1145 148 1191 76 75 76 1131 0 0 547 548 17 41 85 100 73 100 1417 1207 .238 4.21 14.882 10.28 10.677 3.382 34 110 2.908 .51 60 2750 5160 61 67 160 166 0 727 36 691 2.54 719 683 .394 8.981 1.345 3.167 1.345
9 546 633 74 58 472 575 520 520 81 72 446 462 0 0 296 426 35 48 93 98 92 94 1047 908 .821 1.218 1.036 1.12 .967 3.115 79 267 1.501 .64 100 2870 5160 59 69 170 180 0 382 35 347 .735 314 279 1.36 .625 -.444 -.678 -.444
10 335 138 74 56 261 82 286 90 87 71 212 34 0 0 195 144 64 64 90 39 76 19 343 246 3.183 .314 .16 .22 .219 6.073 76 299 .144 .19 110 3020 5160 58 69 184 195 0 83 34 49 .19 54 21 5.274 .097 -2.399 -3.369 -2.399
11 1958 2550 73 59 1885 2491 1949 2445 88 98 1876 2386 0 0 816 1001 67 167 100 100 98 100 4376 4262 .757 1.321 1.272 1.37 1.298 1.644 85 281 1.34 .88 100 3160 5160 59 69 199 209 0 1539 36 1503 .797 1475 1440 1.254 .768 -.326 -.382 -.326
12 4711 12887 72 60 4639 12827 4560 14302 81 96 4488 14242 0 0 3536 8924 42 127 100 100 99 100 17466 18730 .362 2.765 3.173 3.159 2.997 1.583 104 332 2.717 .97 110 3310 5160 58 69 213 224 0 7777 36 7741 1.669 8631 8595 .599 1.915 .739 .937 .739
13 729 1567 71 58 658 1509 648 1547 76 80 577 1489 0 0 486 794 27 104 92 100 91 97 2167 2066 .436 2.293 2.581 2.816 2.254 2.615 81 300 2.247 .85 110 3460 5160 58 69 228 239 0 946 35 911 1.384 934 899 .723 1.557 .469 .639 .469
14 157 1153 71 56 86 1097 106 1037 83 71 35 981 0 0 124 476 75 62 34 100 20 100 1183 1016 .078 12.756 28.029 22.246 24.909 4.699 98 428 20.702 .3 120 3600 5150 57 69 242 254 0 696 34 662 7.698 626 592 .13 16.915 2.944 4.08 2.944
15 247 550 73 56 174 494 192 417 78 66 119 361 0 0 201 358 26 47 75 100 68 96 668 480 .352 2.839 3.034 3.85 3.024 4.96 64 258 5.331 .32 100 3760 5160 59 69 259 269 0 332 34 298 1.713 252 218 .584 1.831 .777 .872 .777
16 22701 10957 73 56 22628 10901 21766 11665 77 71 21693 11609 0 0 18304 8364 23 63 100 100 100 100 33529 33302 2.076 .482 .535 .513 .486 1.642 122 421 .462 .97 130 3900 5160 57 70 271 284 0 6612 34 6578 .291 7040 7006 3.44 .323 -1.782 -1.631 -1.782
17 1323 2225 72 58 1251 2167 1355 2123 83 77 1283 2065 0 0 509 1355 53 88 100 100 100 100 3418 3348 .577 1.732 1.61 1.531 1.526 2.052 67 165 2.257 .79 90 4040 5170 60 69 287 296 0 1343 35 1308 1.045 1281 1246 .957 .971 .064 -.042 .064
18 267 1007 73 58 194 949 203 835 79 80 130 777 0 0 211 721 41 64 75 100 64 97 1143 907 .204 4.892 5.977 7.136 6.057 4.498 85 303 6.76 .56 110 4190 5150 57 68 301 312 0 608 35 573 2.952 504 469 .339 3.607 1.562 1.851 1.562
19 1723 2066 73 58 1650 2008 1710 1951 76 69 1637 1893 0 0 983 1289 22 44 100 100 100 100 3658 3530 .822 1.217 1.156 1.263 1.157 1.958 85 223 1.293 .85 100 4330 5160 59 69 316 326 0 1247 35 1212 .734 1177 1142 1.362 .698 -.445 -.519 -.445
20 936 1467 72 58 864 1409 840 1418 81 74 768 1360 0 0 596 741 53 61 92 100 91 98 2273 2128 .613 1.631 1.771 2.09 1.657 3.006 91 307 1.578 .85 110 4470 5160 58 69 329 340 0 885 35 850 .984 856 821 1.016 1.069 -.023 .096 -.023

Total number of rows: 41472

Table truncated, full table size 9238 Kbytes.




Supplementary data files not provided
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