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Sample GSM40630 Query DataSets for GSM40630
Status Public on Jan 27, 2006
Title array-CGH ME-TMZ
Sample type genomic
 
Channel 1
Source name Cy3: female reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name Cy5: ME-TMZ
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-07/54361.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 = 33.41; Parameter Scan Time = 15:24:39; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 76575; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.13; 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 = 33.41; Parameter Scan Time = 15:24:39; Parameter PMT Volts = 740; Parameter Scan Date = 2004-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 146076; 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) [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
1 455 446 276 244 179 202 445 408 280 256 169 164 0 0 101 135 58 81 86 80 66 50 381 333 .886 1.128 .97 1.044 1.038 2.423 50 251 1.449 .51 90 1460 5910 30 39 21 30 0 431 236 195 1.09 394 158 .917 .937 .125 -.093 .125
2 505 439 273 250 232 189 458 431 281 259 185 181 0 0 164 110 59 76 94 86 75 60 421 366 1.228 .815 .978 .862 .852 2.508 86 265 .706 .55 100 1610 5900 29 39 36 46 0 424 242 183 .787 416 175 1.271 .945 -.346 -.081 -.346
3 565 511 279 264 286 247 508 473 283 272 229 209 0 0 199 187 54 75 93 83 79 63 533 438 1.158 .864 .913 .867 .995 2.704 86 308 .915 .69 110 1760 5900 28 39 50 61 0 494 255 239 .834 457 202 1.199 .882 -.261 -.182 -.261
4 507 443 282 279 225 164 507 444 283 296 225 165 0 0 120 112 62 89 90 80 83 30 389 390 1.372 .729 .733 .746 .742 2.291 30 135 .762 .52 60 1910 5890 30 36 68 74 0 428 270 158 .704 429 159 1.42 .708 -.506 -.497 -.506
5 503 449 279 267 224 182 499 432 281 277 220 165 0 0 108 119 56 85 91 80 85 46 406 385 1.231 .813 .75 .677 .714 2.966 47 239 1.008 .43 90 2050 5900 29 38 80 89 0 434 258 176 .785 417 159 1.274 .725 -.349 -.465 -.349
6 745 841 272 268 473 573 719 828 277 279 447 560 0 0 247 257 64 84 97 100 94 97 1046 1007 .825 1.211 1.253 1.299 1.29 1.905 91 223 1.19 .85 100 2190 5900 29 39 94 104 0 812 259 554 1.17 800 541 .854 1.21 .227 .275 .227
7 296 298 264 265 32 33 283 295 271 275 19 30 0 0 74 92 59 82 30 26 11 7 65 49 .97 1.031 1.579 1.283 1.094 5.373 156 459 3.886 .13 140 2330 5890 26 40 106 120 -50 288 256 32 .996 285 29 1.004 1.525 .609 -.005
8 730 556 261 281 469 275 627 539 268 279 366 258 0 0 291 152 58 82 99 88 97 77 744 624 1.705 .586 .705 .594 .674 3.09 102 208 .442 .59 110 2470 5900 28 39 121 132 0 537 271 266 .566 521 249 1.765 .681 -.82 -.554 -.82
9 570 436 264 277 306 159 569 423 269 280 305 146 0 0 111 99 54 80 99 80 97 43 465 451 1.925 .52 .479 .51 .517 1.987 105 282 .548 .51 120 2630 5900 28 40 137 149 0 421 268 154 .502 409 141 1.992 .462 -.994 -1.113 -.994
10 908 984 275 290 633 694 918 963 280 291 643 673 0 0 220 242 56 83 100 100 100 100 1327 1316 .912 1.096 1.047 1.106 1.076 1.453 119 273 1.103 .89 120 2770 5900 28 40 151 163 0 951 280 670 1.059 930 650 .944 1.011 .083 .016 .083
11 492 441 288 292 204 149 485 440 290 297 197 148 0 0 87 104 60 83 97 75 82 44 353 345 1.369 .73 .751 .733 .854 2.799 74 235 1.046 .39 110 2920 5890 27 38 166 177 0 426 282 144 .706 425 143 1.417 .726 -.503 -.462 -.503
12 637 573 284 279 353 294 609 558 286 288 325 279 0 0 161 155 57 83 99 91 97 81 647 604 1.201 .833 .858 .816 .863 2.288 103 281 .835 .69 120 3070 5900 28 40 181 193 0 554 270 284 .805 539 270 1.243 .829 -.314 -.27 -.314
13 549 485 273 287 276 198 530 478 275 292 257 191 0 0 109 130 55 87 100 79 96 55 474 448 1.394 .717 .743 .643 .738 2.626 114 299 .837 .54 120 3210 5900 28 40 195 207 0 469 277 191 .693 462 185 1.443 .718 -.529 -.478 -.529
14 627 699 278 301 349 398 620 672 285 307 342 371 0 0 147 185 65 93 100 95 94 89 747 713 .877 1.14 1.085 1.114 1.141 1.772 124 421 1.229 .79 130 3360 5900 27 40 209 222 0 675 291 384 1.102 649 358 .908 1.048 .14 .068 .14
15 478 524 269 307 209 217 451 520 275 315 182 213 0 0 96 111 57 93 94 92 87 56 426 395 .963 1.038 1.17 1.128 1.081 2.197 39 223 1.633 .37 100 3500 5890 28 38 225 235 0 506 297 210 1.003 502 206 .997 1.131 .004 .177 .004
16 1235 1195 279 296 956 899 1234 1173 287 303 955 877 0 0 389 297 58 84 100 100 100 100 1855 1832 1.063 .94 .918 .965 .967 1.369 105 251 .903 .93 110 3650 5890 27 38 239 250 0 1154 286 868 .908 1133 847 1.101 .887 -.139 -.173 -.139
17 766 713 294 297 472 416 753 696 298 308 459 399 0 0 184 158 55 86 100 100 99 99 888 858 1.135 .881 .869 .889 .872 1.536 106 271 .862 .83 120 3800 5900 28 40 254 266 0 689 287 402 .851 672 385 1.174 .84 -.232 -.252 -.232
18 738 847 283 304 455 543 738 840 287 310 455 536 0 0 181 222 56 89 100 100 99 96 998 991 .838 1.193 1.178 1.189 1.172 1.705 119 265 1.282 .83 120 3950 5900 28 40 269 281 0 818 294 525 1.153 811 518 .867 1.138 .205 .187 .205
19 1790 1628 276 293 1514 1335 1718 1552 280 299 1442 1259 0 0 703 671 56 90 100 100 100 100 2849 2701 1.134 .882 .873 .886 .881 1.361 112 225 .888 .95 110 4090 5890 27 38 283 294 0 1573 283 1290 .852 1499 1216 1.174 .843 -.231 -.246 -.231
20 645 616 273 290 372 326 649 598 278 290 376 308 0 0 127 127 56 79 99 99 97 95 698 684 1.141 .876 .819 .879 .828 1.659 104 322 .919 .79 120 4240 5890 27 39 298 310 0 595 280 315 .847 578 298 1.181 .791 -.24 -.338 -.24

Total number of rows: 41472

Table truncated, full table size 9718 Kbytes.




Supplementary data files not provided
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