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Sample GSM40631 Query DataSets for GSM40631
Status Public on Jan 27, 2006
Title array-CGH MER-Mock
Sample type genomic
 
Channel 1
Source name Cy3: female reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name Cy5: MER-Mock
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-07/54362.gif
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 = 33.56; Parameter Scan Time = 15:41:06; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 76592; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.11; 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 = 33.56; Parameter Scan Time = 15:41:06; Parameter PMT Volts = 730; Parameter Scan Date = 2004-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 146093; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; 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 24, 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 GPL1831
Series (1)
GSE2221 Drug resistance in glioblastoma

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
1 707 366 282 324 425 42 701 355 299 328 419 31 0 0 211 145 116 82 95 33 77 22 467 450 10.119 .099 .074 .389 .415 4.576 48 142 -.153 -.23 70 1430 5850 25 32 19 26 0 384 340 44 .104 372 32 9.657 .078 -3.272 -3.689 -3.272
2 737 555 287 328 450 227 646 533 293 337 359 205 0 0 267 139 51 82 100 88 100 59 677 564 1.982 .504 .571 .482 .492 2.514 67 224 .453 .67 90 1580 5850 24 33 33 42 0 582 344 238 .529 559 215 1.892 .598 -.92 -.741 -.92
3 670 656 293 313 377 343 510 572 298 322 217 259 0 0 413 309 70 83 97 93 70 68 720 476 1.099 .91 1.194 .995 .957 2.339 93 330 .804 .86 110 1730 5850 23 34 47 58 0 687 328 359 .953 599 271 1.049 1.251 -.069 .323 -.069
4 513 503 300 291 213 212 510 499 301 305 210 208 0 0 115 106 62 75 95 88 76 69 425 418 1.005 .995 .99 1.019 .975 2.173 42 212 1.065 .6 80 1880 5860 26 34 64 72 0 527 305 222 1.043 523 218 .959 1.038 .061 .054 .061
5 464 449 303 314 161 135 460 448 302 318 157 134 0 0 81 105 52 77 92 70 74 44 296 291 1.193 .839 .854 .739 .816 4.162 27 135 1.433 .34 60 2020 5860 27 33 79 85 0 470 329 141 .879 469 140 1.138 .894 -.187 -.161 -.187
6 945 963 289 307 656 656 825 859 303 311 536 552 0 0 435 408 99 78 98 100 93 98 1312 1088 1 1 1.03 1.054 1.052 1.577 97 372 .971 .92 110 2170 5850 23 34 91 102 0 1009 322 687 1.048 900 578 .954 1.079 .067 .11 .067
7 481 412 289 304 192 108 480 408 300 302 191 104 0 0 63 100 61 72 100 62 81 31 300 295 1.778 .563 .545 .662 .83 2.326 16 48 .752 .43 40 2320 5860 28 32 110 114 0 432 319 113 .589 428 109 1.697 .571 -.763 -.81 -.763
8 831 697 295 297 536 400 715 607 300 304 420 310 0 0 365 261 52 75 100 98 100 86 936 730 1.34 .746 .738 .755 .711 1.618 66 271 .704 .84 100 2460 5860 25 35 121 131 0 730 311 419 .782 636 325 1.279 .773 -.355 -.371 -.355
9 520 530 297 307 223 223 503 526 303 306 206 219 0 0 109 116 91 77 93 90 59 67 446 425 1 1 1.063 .921 .957 2.25 103 216 1.094 .66 110 2610 5860 24 35 135 146 0 555 322 234 1.048 551 229 .954 1.114 .067 .156 .067
10 1086 1175 292 305 794 870 1053 1170 297 301 761 865 0 0 287 284 80 76 100 100 100 100 1664 1626 .913 1.096 1.137 1.098 1.108 1.344 110 310 1.093 .94 120 2750 5850 23 35 149 161 0 1231 320 912 1.148 1226 906 .871 1.191 .199 .252 .199
11 454 428 284 292 170 136 450 440 287 295 166 148 0 0 84 104 54 69 92 71 73 52 306 314 1.25 .8 .892 .953 1.028 3.415 57 219 1.031 .27 110 2910 5860 24 35 165 176 0 448 306 143 .838 461 155 1.193 .934 -.255 -.098 -.255
12 714 701 281 287 433 414 720 696 285 290 439 409 0 0 159 157 54 71 100 100 97 97 847 848 1.046 .956 .932 .962 .933 1.641 99 244 .949 .84 110 3040 5850 23 34 178 189 0 735 301 434 1.002 729 429 .998 .976 .003 -.035 .003
13 638 750 283 290 355 460 607 723 279 297 324 433 0 0 135 175 50 82 100 100 98 99 815 757 .772 1.296 1.336 1.296 1.237 1.603 101 259 1.329 .84 110 3190 5850 23 34 193 204 0 786 304 482 1.358 758 454 .737 1.4 .441 .486 .441
14 778 839 278 298 500 541 760 812 281 302 482 514 0 0 179 189 62 81 100 100 100 100 1041 996 .924 1.082 1.066 1.1 1.08 1.515 107 360 1.1 .86 120 3340 5850 23 35 208 220 0 879 312 567 1.134 851 539 .882 1.117 .181 .16 .181
15 472 443 278 294 194 149 462 447 279 296 184 153 0 0 82 96 63 73 94 80 79 52 343 337 1.302 .768 .832 .689 .73 2.439 92 339 .969 .56 120 3480 5850 23 35 222 234 0 464 308 156 .805 468 160 1.243 .871 -.313 -.199 -.313
16 1480 1391 277 302 1203 1089 1361 1262 275 308 1084 960 0 0 732 527 50 76 100 100 100 100 2292 2044 1.105 .905 .886 .974 .911 1.448 98 203 .816 .94 100 3630 5850 24 34 238 248 0 1458 316 1141 .949 1322 1006 1.054 .928 -.076 -.108 -.076
17 1455 1196 280 311 1175 885 1458 1115 282 315 1178 804 0 0 388 304 49 78 100 100 100 100 2060 1982 1.328 .753 .683 .757 .73 1.308 111 288 .74 .95 120 3780 5850 23 35 252 264 0 1253 326 927 .789 1168 842 1.267 .715 -.341 -.484 -.341
18 1524 1583 279 305 1245 1278 1607 1549 287 311 1328 1244 0 0 439 410 68 79 100 100 100 100 2523 2572 .974 1.027 .937 1.053 .995 1.359 120 280 .993 .94 120 3920 5850 23 35 266 278 0 1659 320 1339 1.076 1623 1304 .93 .982 .105 -.027 .105
19 3533 3515 279 319 3254 3196 3730 3639 287 324 3451 3320 0 0 1493 1282 57 86 100 100 100 100 6450 6771 1.018 .982 .962 1.022 .979 1.248 106 220 .942 .98 110 4060 5850 23 34 280 291 0 3683 334 3349 1.029 3813 3479 .972 1.008 .041 .012 .041
20 1357 1134 294 333 1063 801 1353 1130 299 338 1059 797 0 0 316 202 60 87 100 100 100 100 1864 1856 1.327 .754 .753 .768 .762 1.375 105 228 .713 .91 110 4210 5850 23 34 295 306 0 1188 349 839 .79 1184 835 1.266 .789 -.341 -.343 -.341

Total number of rows: 41472

Table truncated, full table size 9791 Kbytes.




Supplementary data files not provided
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