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Sample GSM40632 Query DataSets for GSM40632
Status Public on Jan 27, 2006
Title array-CGH MER-TMZ
Sample type genomic
 
Channel 1
Source name Cy3: female reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name Cy5: MER-TMZ
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-07/54370.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 = 34.11; Parameter Scan Time = 16:29:08; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 76640; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.06; 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 = 34.11; Parameter Scan Time = 16:29:08; Parameter PMT Volts = 750; Parameter Scan Date = 2004-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 146141; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.61; 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) [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 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
1 508 410 275 271 233 139 496 420 279 274 221 149 0 0 129 108 50 85 94 71 91 37 372 370 1.676 .597 .674 .711 .8 3.02 35 237 .689 .33 80 1420 5490 25 33 18 26 0 402 266 136 .585 412 146 1.708 .662 -.772 -.596 -.772
2 552 357 264 259 288 98 526 334 269 261 262 75 0 0 172 107 44 83 96 49 93 27 386 337 2.939 .34 .286 .385 .363 3.264 61 200 .305 .33 90 1580 5480 23 32 33 42 0 350 254 96 .334 328 74 2.995 .281 -1.582 -1.832 -1.582
3 530 464 262 255 268 209 488 441 265 262 226 186 0 0 173 143 43 82 99 85 92 58 477 412 1.282 .78 .823 .797 .855 2.408 117 333 .777 .73 120 1720 5480 22 34 46 58 0 455 250 205 .765 433 183 1.307 .808 -.386 -.308 -.386
4 441 388 260 255 181 133 436 386 264 266 176 131 0 0 106 89 46 83 93 67 82 34 314 307 1.361 .735 .744 .702 .612 2.782 46 269 1.222 .35 100 1870 5480 23 33 62 72 0 381 250 131 .721 379 129 1.387 .73 -.472 -.453 -.472
5 426 368 270 274 156 94 435 358 270 270 165 84 0 0 84 110 49 73 90 57 63 27 250 249 1.66 .603 .509 .89 1.039 3.134 33 119 2.637 .11 60 2000 5480 25 31 77 83 0 361 269 92 .591 351 82 1.691 .5 -.758 -1.001 -.758
6 623 620 263 263 360 357 590 574 262 268 327 311 0 0 233 209 44 78 100 97 95 92 717 638 1.008 .992 .951 1.044 1.029 1.8 90 324 1.012 .79 110 2150 5470 21 32 89 100 0 608 258 350 .973 563 305 1.028 .933 -.039 -.1 -.039
7 279 266 263 250 16 16 266 259 265 259 3 9 0 0 53 86 44 77 26 17 11 7 32 12 1 1 3 1.197 1.105 4.507 156 527 30.133 .03 140 2300 5470 20 34 103 117 -50 261 245 16 .981 254 9 1.019 2.944 1.558 -.027
8 690 596 269 257 421 339 616 541 270 267 347 284 0 0 264 196 43 80 100 97 100 86 760 631 1.242 .805 .818 .838 .787 1.856 43 94 .755 .81 70 2450 5490 25 32 121 128 0 585 252 333 .79 531 279 1.266 .803 -.34 -.316 -.34
9 447 378 269 250 178 128 450 374 268 254 181 124 0 0 87 89 45 74 94 73 84 39 306 305 1.391 .719 .685 .732 .647 2.491 84 340 .993 .44 120 2590 5480 22 34 133 145 0 371 245 126 .706 367 122 1.417 .672 -.503 -.573 -.503
10 852 669 255 257 597 412 809 632 259 260 554 375 0 0 268 204 58 77 100 97 99 96 1009 929 1.449 .69 .677 .664 .711 1.97 108 296 .678 .84 120 2740 5480 22 34 148 160 0 656 252 404 .677 620 368 1.477 .664 -.562 -.59 -.562
11 363 294 249 250 114 44 348 291 252 261 99 41 0 0 95 101 47 83 77 30 53 7 158 140 2.591 .386 .414 .695 .776 3.496 156 374 1.011 .62 140 2880 5500 23 37 161 175 -50 289 245 43 .379 286 40 2.64 .406 -1.299 -1.401
12 655 629 250 246 405 383 618 592 254 256 368 346 0 0 165 177 45 83 100 100 100 94 788 714 1.057 .946 .94 .932 .954 1.655 96 249 1.009 .8 110 3020 5470 21 32 176 187 0 617 241 376 .928 581 340 1.078 .923 -.108 -.116 -.108
13 566 642 254 242 312 400 560 642 255 257 306 400 0 0 92 169 45 87 100 99 100 93 712 706 .78 1.282 1.307 1.216 1.243 1.6 103 253 1.467 .82 110 3170 5470 21 32 191 202 0 630 237 393 1.258 630 393 .795 1.283 .331 .359 .331
14 863 952 250 251 613 701 843 932 253 262 593 681 0 0 195 220 43 83 100 100 100 100 1314 1274 .874 1.144 1.148 1.152 1.127 1.442 123 335 1.155 .89 120 3320 5470 21 33 206 218 0 934 246 688 1.122 915 668 .891 1.127 .166 .172 .166
15 467 396 249 250 218 146 455 389 251 259 206 139 0 0 94 120 42 83 96 67 93 38 364 345 1.493 .67 .675 .614 .735 2.943 113 303 .918 .45 120 3470 5470 21 33 221 233 0 389 245 143 .657 382 136 1.522 .662 -.606 -.595 -.606
16 1836 1523 248 255 1588 1268 1706 1381 252 263 1458 1126 0 0 862 644 43 81 100 100 100 100 2856 2584 1.252 .798 .772 .829 .799 1.401 113 287 .782 .95 120 3610 5470 21 33 235 247 0 1495 250 1244 .784 1355 1105 1.276 .758 -.352 -.4 -.352
17 825 590 252 248 573 342 798 555 256 258 546 307 0 0 215 162 52 85 100 97 100 87 915 853 1.675 .597 .562 .569 .572 1.714 114 286 .584 .8 120 3760 5470 21 33 250 262 0 579 243 336 .586 545 301 1.707 .552 -.772 -.858 -.772
18 1161 1043 249 244 912 799 1187 1037 254 252 938 793 0 0 288 232 43 87 100 100 100 100 1711 1731 1.141 .876 .845 .892 .852 1.429 108 208 .846 .91 110 3900 5470 21 32 264 275 0 1024 239 784 .86 1018 778 1.163 .83 -.218 -.269 -.218
19 2096 1677 248 253 1848 1424 1948 1533 254 259 1700 1280 0 0 1025 726 47 83 100 100 100 100 3272 2980 1.298 .771 .753 .798 .78 1.323 106 219 .743 .97 110 4040 5470 21 32 278 289 0 1646 248 1397 .756 1504 1256 1.322 .739 -.403 -.437 -.403
20 904 668 244 254 660 414 923 656 251 259 679 402 0 0 187 133 46 82 100 100 100 100 1074 1081 1.594 .627 .592 .624 .62 1.477 99 231 .611 .85 110 4190 5470 21 32 293 304 0 656 249 406 .616 644 394 1.625 .581 -.7 -.783 -.7

Total number of rows: 41472

Table truncated, full table size 9768 Kbytes.




Supplementary data files not provided
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