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Sample GSM148712 Query DataSets for GSM148712
Status Public on Oct 03, 2007
Title PT07_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52826.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT07_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT07_2 DNA
Prostate genomic DNA; LabeledExtract: 52826.Channel_2
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe
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 = 38.85; Parameter Scan Time = 10:33:32; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166598; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe
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 = 38.85; Parameter Scan Time = 10:33:32; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531502; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.05; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe
Description Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52826.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 06, 2006
Last update date Oct 03, 2007
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL4639
Series (1)
GSE6469 Array CGH data of 64 prostate cancer specimens

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
LOG_RAT2N_MEAN 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
VALUE 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

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 LOG_RAT2N_MEAN VALUE
1 381 323 181 200 200 123 378 323 182 203 197 123 0 0 61 82 40 59 100 84 96 53 323 320 1.626 .615 .624 .628 .712 2.314 32 220 .763 .283 70 1880 6390 63 70 36 43 0 362 224 138 .69 362 138 1.45 .7 -.536 -.514
2 526 430 178 190 348 240 510 420 182 195 332 230 0 0 133 128 41 56 98 92 96 84 588 562 1.45 .69 .693 .626 .73 1.924 52 295 .74 .649 80 2030 6400 64 72 51 59 0 482 213 269 .773 471 258 1.293 .777 -.371 -.364
3 446 328 178 202 268 126 451 327 181 209 273 125 0 0 70 75 40 60 100 78 100 50 394 398 2.127 .47 .458 .42 .506 2.448 32 208 .521 .27 70 2180 6400 64 71 66 73 0 368 227 141 .527 367 140 1.896 .514 -.923 -.961
4 355 338 173 199 182 139 343 318 176 203 170 119 0 0 76 114 39 56 100 75 93 50 321 289 1.309 .764 .7 .65 .732 2.63 32 226 .898 .303 70 2310 6390 63 70 79 86 0 379 223 156 .857 357 133 1.167 .785 -.223 -.349
5 363 340 168 190 195 150 367 351 172 193 199 161 0 0 83 68 48 63 92 94 88 61 345 360 1.3 .769 .809 .836 .698 2.39 52 294 .776 .32 80 2470 6390 63 71 95 103 0 381 213 168 .863 394 181 1.159 .907 -.213 -.14
6 442 358 177 202 265 156 378 313 180 205 201 111 0 0 376 229 40 60 93 59 90 46 421 312 1.699 .589 .552 .513 .641 3.37 32 218 .758 .507 70 2610 6390 63 70 109 116 0 402 227 175 .66 351 124 1.515 .619 -.599 -.691
7 387 316 182 181 205 135 405 309 184 190 223 128 0 0 61 75 37 60 96 87 96 50 340 351 1.519 .659 .574 .545 .714 2.532 32 227 .869 .354 70 2760 6390 63 70 124 131 0 354 203 151 .739 347 144 1.354 .644 -.437 -.635
8 468 366 187 199 281 167 470 334 188 198 283 135 0 0 100 96 42 63 100 93 100 56 448 418 1.683 .594 .477 .551 .586 1.652 32 214 .66 .482 70 2900 6390 63 70 138 145 0 410 223 187 .667 375 151 1.5 .535 -.585 -.902
9 376 403 186 194 190 209 366 389 187 198 180 195 0 0 75 89 38 61 100 98 96 78 399 375 .909 1.1 1.083 1.085 1.132 1.731 52 324 1.223 .471 90 3050 6390 62 71 152 161 0 452 218 234 1.234 436 219 .811 1.215 .303 .281
10 482 494 180 190 302 304 473 487 182 193 293 297 0 0 97 108 40 58 100 98 100 98 606 590 .993 1.007 1.014 .975 .998 1.64 52 300 1.114 .624 90 3200 6390 62 71 167 176 0 554 213 341 1.129 546 333 .886 1.137 .175 .185
11 353 343 181 196 172 147 357 338 186 200 176 142 0 0 68 75 42 63 98 84 94 55 319 318 1.17 .855 .807 .748 .755 1.998 52 312 1.078 .317 90 3340 6390 62 71 181 190 0 385 220 165 .959 379 159 1.043 .905 -.061 -.144
12 431 450 177 195 254 255 435 451 185 198 258 256 0 0 85 93 43 61 100 98 100 90 509 514 .996 1.004 .992 .986 .999 1.738 52 337 1.094 .532 90 3490 6390 62 71 196 205 0 505 219 286 1.126 506 287 .888 1.113 .171 .154
13 432 446 179 193 253 253 430 441 195 205 251 248 0 0 73 99 180 111 82 90 7 63 506 499 1 1 .988 .947 .997 1.646 52 313 1.333 .422 90 3640 6390 62 71 211 220 0 500 216 284 1.122 495 278 .892 1.108 .165 .148
14 511 553 178 209 333 344 504 536 211 249 326 327 0 0 88 100 290 425 73 19 1 0 677 653 .968 1.033 1.003 1.022 1.048 1.435 52 324 .706 .507 90 3780 6380 61 70 225 234 0 620 234 386 1.159 601 367 .863 1.125 .212 .17
15 321 336 169 194 152 142 312 346 196 237 143 152 0 0 84 89 256 454 13 0 0 0 294 295 1.07 .934 1.063 1.061 1.015 1.752 52 273 1.792 .907 90 3940 6400 63 72 241 250 0 377 218 159 1.048 388 170 .954 1.192 .067 .254
16 842 1531 170 186 672 1345 777 1111 176 193 607 925 0 0 618 3289 66 65 97 97 95 96 2017 1532 .5 2.001 1.524 1.544 1.56 1.686 80 346 4.88 .691 100 4080 6390 62 72 255 265 0 1717 209 1508 2.245 1246 1037 .445 1.709 1.167 .773
17 583 636 173 184 410 452 537 590 182 191 364 406 0 0 261 253 75 65 100 100 98 100 862 770 .907 1.102 1.115 1.107 1.116 1.453 52 264 1.107 .698 90 4220 6390 62 71 269 278 0 713 206 507 1.236 662 455 .809 1.251 .306 .323
18 549 614 171 183 378 431 535 615 189 192 364 432 0 0 133 142 196 69 90 100 38 100 809 796 .877 1.14 1.187 1.172 1.174 1.598 52 301 .574 .3 90 4360 6390 62 71 283 292 0 689 205 483 1.279 690 485 .782 1.331 .355 .413
19 1068 1305 169 193 899 1112 1034 1301 175 204 865 1108 0 0 260 261 44 70 100 100 100 100 2011 1973 .808 1.237 1.281 1.261 1.243 1.322 52 324 1.228 .837 90 4510 6380 61 70 298 307 0 1464 216 1247 1.387 1459 1243 .721 1.437 .472 .523
20 503 540 165 191 338 349 487 522 170 197 322 331 0 0 94 102 43 60 100 100 100 100 687 653 .968 1.033 1.028 1.025 1.022 1.459 52 301 1.113 .671 90 4660 6390 62 71 313 322 0 606 214 391 1.158 585 371 .864 1.153 .212 .205

Total number of rows: 41472

Table truncated, full table size 9240 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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