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Sample GSM40682 Query DataSets for GSM40682
Status Public on Jan 27, 2006
Title expression array - AOA6
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AOA6
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56927
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 = 31.61; Parameter Scan Time = 20:25:51; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12074; 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 = 31.61; Parameter Scan Time = 20:25:51; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185679; 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
1 639 623 124 53 515 570 509 406 133 61 385 353 0 0 422 779 63 44 100 100 90 90 1085 738 .904 1.107 .917 .891 .948 3.2 40 173 2.21 .49 70 1800 5330 73 80 60 67 0 352 30 322 .625 229 199 1.601 .517 -.679 -.951 -.679
2 9738 1182 119 53 9619 1129 7734 744 127 64 7615 691 0 0 8729 1118 50 59 100 83 100 74 10748 8306 8.52 .117 .091 .099 .11 2.644 85 357 .111 .9 100 1940 5330 72 82 73 83 0 667 30 637 .066 420 390 15.1 .051 -3.916 -4.288 -3.916
3 1559 1099 122 56 1437 1043 1471 979 133 63 1349 923 0 0 902 808 69 38 100 100 92 96 2480 2272 1.378 .726 .684 .659 .751 3.019 27 139 .741 .77 60 2090 5340 75 81 90 96 0 620 32 589 .41 552 521 2.442 .386 -1.288 -1.373 -1.288
4 949 422 121 55 828 367 658 319 125 74 537 264 0 0 975 448 31 95 95 65 90 57 1195 801 2.256 .443 .492 .393 .438 3.931 40 119 .22 .39 60 2240 5340 75 81 105 111 0 238 31 207 .25 180 149 3.998 .277 -1.999 -1.85 -1.999
5 452 198 122 58 330 140 332 104 131 76 210 46 0 0 586 213 73 66 78 40 65 31 470 256 2.357 .424 .219 .403 .432 7.977 47 241 .13 .28 80 2390 5330 73 81 119 127 0 112 33 79 .239 59 26 4.177 .124 -2.063 -3.016 -2.063
6 625 251 122 57 503 194 604 189 129 72 482 132 0 0 260 202 50 63 96 57 92 50 697 614 2.593 .386 .274 .256 .334 4.484 28 135 .376 .6 60 2520 5340 75 81 133 139 0 142 32 109 .218 107 74 4.595 .155 -2.2 -2.694 -2.2
7 734 484 121 51 613 433 677 334 130 60 556 283 0 0 421 613 52 32 96 89 96 85 1046 839 1.416 .706 .509 .454 .391 4.658 28 65 1.221 .37 50 2670 5330 74 79 148 153 0 273 29 244 .399 188 160 2.509 .287 -1.327 -1.8 -1.327
8 630 2280 118 54 512 2226 590 2291 125 60 472 2237 0 0 401 1653 46 22 96 96 89 96 2738 2709 .23 4.348 4.739 3.925 5.011 2.984 28 141 4.855 .86 60 2820 5340 75 81 163 169 0 1286 30 1256 2.453 1293 1262 .408 2.674 1.295 1.419 1.295
9 1404 2660 115 54 1289 2606 1365 2610 124 62 1250 2556 0 0 814 1241 45 34 96 100 96 100 3895 3806 .495 2.022 2.045 2.398 2.071 2.846 65 240 2.202 .75 90 2970 5330 72 81 176 185 0 1501 30 1470 1.141 1473 1442 .877 1.154 .19 .206 .19
10 676 403 116 53 560 350 545 196 124 68 429 143 0 0 519 513 43 86 96 63 89 46 910 572 1.6 .625 .333 .352 .451 8.255 65 215 .439 .19 90 3110 5330 72 81 190 199 0 227 30 197 .353 111 81 2.836 .188 -1.504 -2.411 -1.504
11 4110 8148 120 55 3990 8093 3852 8408 128 67 3732 8353 0 0 2121 3375 48 78 98 100 98 100 12083 12085 .493 2.028 2.238 2.115 2.234 1.672 72 225 2.082 .86 90 3250 5320 71 80 204 213 0 4598 31 4566 1.144 4744 4713 .874 1.263 .195 .337 .195
12 10209 30974 117 56 10092 30918 11201 36601 124 62 11084 36545 0 0 4919 13780 42 31 100 100 100 100 41010 47629 .326 3.064 3.297 3.438 3.033 1.914 69 250 3.153 .94 90 3390 5320 71 80 218 227 0 17477 32 17445 1.729 20652 20621 .578 1.86 .79 .896 .79
13 1412 2805 118 57 1294 2748 1245 2894 122 73 1127 2837 0 0 900 1535 42 60 93 100 93 100 4042 3964 .471 2.124 2.517 2.554 2.193 2.399 62 250 2.215 .81 90 3550 5320 71 80 234 243 0 1583 32 1551 1.198 1633 1601 .835 1.42 .261 .506 .261
14 307 1906 116 55 191 1851 212 1600 125 66 96 1545 0 0 281 929 71 53 53 100 41 100 2042 1641 .103 9.691 16.094 15.238 12.168 4.46 81 307 10.784 .49 100 3690 5320 71 81 248 258 0 1075 31 1044 5.468 903 872 .183 9.081 2.451 3.183 2.451
15 596 3595 113 56 483 3539 520 3486 123 67 407 3430 0 0 608 1788 54 53 70 100 64 100 4022 3837 .136 7.327 8.428 12.976 9.841 4.622 74 188 9.208 .49 90 3830 5330 72 81 262 271 0 2028 32 1997 4.134 1967 1935 .242 4.755 2.048 2.25 2.048
16 27701 23990 116 55 27585 23935 35421 26589 127 73 35305 26534 0 0 21217 18270 58 90 100 100 100 100 51520 61839 1.152 .868 .752 .992 .88 1.791 98 334 .862 .98 110 3980 5320 70 81 276 287 0 13536 31 13505 .49 15003 14972 2.043 .424 -1.03 -1.238 -1.03
17 2512 3813 117 56 2395 3757 2202 3645 120 68 2085 3589 0 0 1553 2108 27 47 98 100 98 100 6152 5674 .637 1.569 1.721 1.724 1.566 2.214 61 233 1.592 .85 90 4130 5320 71 80 292 301 0 2151 32 2120 .885 2057 2025 1.13 .971 -.176 -.042 -.176
18 540 2371 114 56 426 2315 425 2166 123 65 311 2110 0 0 465 1183 37 39 86 100 78 100 2741 2421 .184 5.434 6.785 8.279 6.415 3.722 61 186 6.902 .53 80 4270 5320 72 80 307 315 0 1338 32 1306 3.066 1222 1191 .326 3.828 1.616 1.937 1.616
19 2442 3420 115 55 2327 3365 2369 3174 123 68 2254 3119 0 0 1335 1916 46 45 100 100 100 100 5692 5373 .692 1.446 1.384 1.489 1.445 2.014 78 283 1.53 .85 100 4420 5320 71 81 321 331 0 1930 31 1899 .816 1791 1760 1.226 .781 -.293 -.357 -.293
20 1618 2815 114 54 1504 2761 1335 2681 119 66 1221 2627 0 0 944 1437 49 51 100 100 100 100 4265 3848 .545 1.836 2.152 1.925 1.948 2.133 73 216 2.012 .75 90 4550 5320 71 80 334 343 0 1588 30 1558 1.036 1513 1482 .965 1.214 .051 .28 .051

Total number of rows: 41472

Table truncated, full table size 9413 Kbytes.




Supplementary data files not provided

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