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Sample GSM40711 Query DataSets for GSM40711
Status Public on Jan 27, 2006
Title expression array - AOA4
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AOA4
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56938
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 = 31.67; Parameter Scan Time = 21:02:55; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12111; 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 = 31.67; Parameter Scan Time = 21:02:55; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185716; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; 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
1 570 432 110 49 460 383 470 434 115 53 360 385 0 0 348 217 42 16 100 100 100 97 843 745 1.201 .833 1.069 .801 .968 2.133 47 151 .68 .76 70 1710 5130 53 60 51 58 0 284 32 252 .547 285 253 1.829 .702 -.871 -.51 -.871
2 6234 1843 108 51 6126 1792 2200 766 115 60 2092 715 0 0 6638 1998 38 55 99 92 97 85 7918 2807 3.419 .293 .342 .298 .29 2.57 116 497 .287 .96 130 1860 5130 50 63 63 76 0 1211 33 1177 .192 503 470 5.204 .224 -2.38 -2.155 -2.38
3 804 361 108 53 696 308 519 327 116 61 411 274 0 0 775 239 39 31 97 86 97 81 1004 685 2.26 .443 .667 .403 .403 2.564 43 159 .308 .81 70 2010 5130 53 60 81 88 0 237 35 202 .291 215 180 3.44 .438 -1.783 -1.191 -1.783
4 682 158 107 52 575 106 704 136 113 54 597 84 0 0 318 113 36 13 100 80 100 68 681 681 5.425 .184 .141 .144 .169 3.446 45 167 .144 .55 70 2160 5130 53 60 96 103 0 104 34 70 .121 89 55 8.258 .092 -3.046 -3.436 -3.046
5 391 130 105 52 286 78 337 100 112 61 232 48 0 0 182 91 36 37 100 52 97 35 364 280 3.667 .273 .207 .202 .329 4.122 42 226 .195 .38 80 2300 5140 54 62 110 118 0 85 34 51 .179 66 32 5.582 .136 -2.481 -2.879 -2.481
6 617 493 110 52 507 441 552 418 115 62 442 366 0 0 363 316 34 33 100 97 100 94 948 808 1.15 .87 .828 .807 .952 2.37 36 137 .817 .65 60 2440 5130 54 60 125 131 0 324 34 290 .571 275 240 1.75 .544 -.808 -.879 -.808
7 439 339 109 56 330 283 382 315 119 60 273 259 0 0 235 219 48 25 96 88 76 88 613 532 1.166 .858 .949 .769 .859 3.535 26 162 .827 .67 60 2580 5120 53 59 139 145 0 223 37 186 .563 207 170 1.775 .623 -.828 -.682 -.828
8 277 519 104 55 173 464 239 430 109 58 135 375 0 0 156 376 35 19 75 100 65 100 637 510 .373 2.682 2.778 3.203 2.874 3.226 41 160 2.98 .81 70 2730 5130 53 60 153 160 0 341 36 305 1.762 282 246 .568 1.825 .817 .868 .817
9 830 833 106 55 724 778 810 827 110 61 704 772 0 0 421 399 32 24 97 100 96 100 1502 1476 .931 1.075 1.097 1.126 1.053 2.25 79 293 1.035 .85 100 2880 5130 52 62 167 177 0 547 36 511 .706 543 507 1.417 .72 -.503 -.473 -.503
10 510 262 105 53 405 209 420 238 114 60 315 185 0 0 267 167 44 50 98 87 98 68 614 500 1.938 .516 .587 .469 .53 3.087 74 265 .359 .44 100 3020 5130 52 62 181 191 0 172 35 137 .339 156 122 2.95 .386 -1.561 -1.374 -1.561
11 2474 3373 103 55 2371 3318 2535 3392 113 63 2432 3337 0 0 1380 1677 45 52 100 100 98 100 5689 5769 .715 1.399 1.372 1.476 1.392 1.813 82 261 1.385 .9 100 3170 5130 52 62 196 206 0 2216 36 2179 .919 2228 2192 1.088 .901 -.122 -.15 -.122
12 6496 11663 105 55 6391 11608 6205 11526 112 60 6100 11471 0 0 5046 8356 39 25 97 100 96 100 17999 17571 .551 1.816 1.88 2.064 1.872 1.733 104 391 1.764 .98 120 3310 5130 51 63 209 221 0 7661 36 7625 1.193 7571 7535 .838 1.235 .255 .305 .255
13 880 2110 103 55 777 2055 746 2248 125 60 643 2193 0 0 593 939 117 26 91 100 85 100 2832 2836 .378 2.645 3.411 3.08 2.689 2.474 85 254 2.582 .79 100 3460 5130 52 62 225 235 0 1386 36 1350 1.737 1477 1440 .576 2.24 .797 1.164 .797
14 250 1512 103 56 147 1456 168 1504 114 67 65 1448 0 0 199 732 76 41 48 100 33 100 1603 1513 .101 9.905 22.277 14.716 15.033 4.874 87 282 15.771 .37 100 3610 5130 52 62 240 250 0 993 37 956 6.506 988 951 .154 14.632 2.702 3.871 2.702
15 220 1388 103 56 117 1332 181 1298 112 63 78 1242 0 0 129 539 60 33 59 100 31 100 1449 1320 .088 11.385 15.923 15.94 14.174 3.219 77 188 16.125 .38 90 3750 5130 52 61 254 263 0 912 37 875 7.478 853 816 .134 10.459 2.903 3.387 2.903
16 38670 25397 102 54 38568 25343 52124 27052 111 59 52022 26998 20 0 26726 17778 52 24 100 100 100 100 63911 79020 1.522 .657 .519 .681 .671 1.401 108 388 .658 .99 120 3900 5130 51 63 268 280 0 16682 35 16646 .432 17769 17733 2.317 .341 -1.212 -1.553 -1.212
17 2026 3566 105 54 1921 3512 1950 3805 111 59 1845 3751 0 0 907 1184 46 26 100 100 100 100 5433 5596 .547 1.828 2.033 1.924 1.961 1.746 71 170 1.853 .85 80 4050 5120 52 60 285 293 0 2342 35 2307 1.201 2499 2464 .833 1.335 .264 .417 .264
18 383 2800 106 54 277 2746 313 2841 112 59 207 2787 0 0 238 1097 46 25 86 100 78 100 3023 2994 .101 9.913 13.464 13.425 13.066 2.714 87 275 10.917 .67 110 4190 5130 51 62 297 308 0 1839 35 1804 6.512 1866 1831 .154 8.844 2.703 3.145 2.703
19 2400 2535 102 57 2298 2478 2415 2631 108 64 2313 2574 0 0 1132 1195 44 33 100 100 100 100 4776 4887 .927 1.078 1.113 1.029 1.078 1.738 79 226 1.084 .89 100 4340 5130 52 62 313 323 0 1665 37 1628 .708 1728 1691 1.412 .731 -.498 -.452 -.498
20 1725 1922 104 57 1621 1865 1746 1993 115 64 1642 1936 0 0 797 902 57 31 100 100 100 100 3486 3578 .869 1.151 1.179 1.144 1.179 1.649 86 301 1.17 .89 110 4480 5130 51 62 326 337 0 1262 37 1225 .756 1309 1272 1.323 .774 -.404 -.369 -.404

Total number of rows: 41472

Table truncated, full table size 9423 Kbytes.




Supplementary data files not provided
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