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Sample GSM148708 Query DataSets for GSM148708
Status Public on Oct 03, 2007
Title PT19_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52822.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT19_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT19_2 DNA
Prostate genomic DNA; LabeledExtract: 52822.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 = 39.06; Parameter Scan Time = 11:01:54; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166624; 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 = 39.06; Parameter Scan Time = 11:01:54; Parameter PMT Volts = 730; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531527; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; 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/2004-06/52822.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
1 413 173 187 173 226 0 406 184 190 178 219 11 0 0 74 64 48 67 100 12 100 3 226 230 null null .05 .149 .174 2.348 32 170 -1 0 60 1930 6790 104 110 42 48 0 227 227 0 null 241 14 null .066 null -3.924
2 627 314 180 185 447 129 594 307 185 190 414 122 0 0 145 113 39 70 100 65 100 37 576 536 3.465 .289 .295 .26 .297 2.314 32 230 .279 .254 70 2080 6790 103 110 56 63 0 412 243 169 .378 403 160 2.643 .386 -1.402 -1.372
3 517 239 182 182 335 57 514 226 187 191 332 44 0 0 64 90 43 69 100 40 100 21 392 376 5.877 .17 .133 .228 .245 2.555 32 227 .122 .027 70 2230 6790 103 110 71 78 0 313 239 75 .223 296 58 4.482 .174 -2.164 -2.525
4 522 209 187 174 335 35 511 192 188 181 324 18 0 0 76 66 38 63 100 31 100 6 370 342 9.571 .104 .056 .137 .171 3.107 32 226 .067 .017 70 2370 6790 103 110 85 92 0 274 228 46 .137 252 24 7.3 .073 -2.868 -3.779
5 389 224 186 192 203 32 397 213 184 194 211 21 0 0 66 74 40 68 100 25 100 9 235 232 6.344 .158 .1 .207 .226 3.469 32 176 .083 .004 60 2520 6790 104 110 101 107 0 294 252 42 .207 279 28 4.838 .13 -2.274 -2.938
6 378 235 193 186 185 49 370 236 200 187 177 50 0 0 51 55 57 67 100 33 100 0 234 227 3.776 .265 .282 .349 .418 1.963 12 98 37.55 .001 50 2680 6780 103 108 117 122 0 308 244 64 .347 309 66 2.879 .37 -1.526 -1.433
7 390 184 185 191 205 -7 392 170 189 198 207 -21 0 0 66 75 45 69 100 15 96 3 198 186 null null null .259 .371 2.752 32 170 24.93 .001 60 2810 6800 105 111 130 136 0 241 250 -9 null 223 -28 null null null null
8 495 191 187 180 308 11 478 185 191 195 291 5 0 0 96 73 46 178 100 3 100 0 319 296 28 .036 .017 .152 .172 2.298 32 212 1.36 .059 70 2960 6790 103 110 144 151 0 250 236 14 .047 243 7 21.354 .023 -4.416 -5.472
9 444 364 187 177 257 187 440 357 192 183 253 180 0 0 71 98 44 75 100 86 100 55 444 433 1.374 .728 .711 .645 .746 1.922 52 304 .84 .418 90 3100 6790 102 111 157 166 0 477 232 245 .954 468 236 1.048 .933 -.068 -.1
10 563 409 184 182 379 227 572 391 192 186 388 209 0 0 106 97 42 78 100 96 100 75 606 597 1.67 .599 .539 .58 .592 1.588 52 301 .698 .458 90 3240 6790 102 111 171 180 0 536 239 298 .785 513 274 1.273 .706 -.349 -.502
11 448 343 188 180 260 163 441 342 191 190 253 162 0 0 71 92 43 72 100 82 100 61 423 415 1.595 .627 .64 .58 .641 1.892 52 300 .792 .339 90 3390 6800 103 112 186 195 0 450 236 214 .822 448 212 1.217 .84 -.283 -.252
12 556 460 187 182 369 278 553 469 193 194 366 287 0 0 89 137 46 74 100 94 100 76 647 653 1.327 .753 .784 .682 .729 1.895 52 316 .87 .531 90 3540 6790 102 111 201 210 0 603 239 365 .988 615 376 1.012 1.028 -.018 .04
13 573 432 186 182 387 250 553 409 191 188 367 227 0 0 124 148 41 70 100 96 100 86 637 594 1.548 .646 .619 .589 .592 1.792 52 288 .685 .523 90 3680 6790 102 111 215 224 0 566 239 328 .847 536 298 1.181 .811 -.24 -.302
14 673 398 192 184 481 214 642 384 193 188 450 200 0 0 143 133 42 64 100 88 100 73 695 650 2.248 .445 .444 .4 .407 1.858 52 311 .455 .488 90 3820 6790 102 111 229 238 0 522 241 281 .583 504 262 1.714 .583 -.778 -.779
15 433 428 195 190 238 238 411 424 196 195 216 234 0 0 80 110 41 68 100 94 100 82 476 450 1 1 1.083 .921 .879 2.071 52 299 1.143 .428 90 3980 6790 102 111 245 254 0 561 249 312 1.311 556 307 .763 1.42 .391 .506
16 1209 1142 192 192 1017 950 1235 1142 195 201 1043 950 0 0 395 339 43 71 98 98 98 97 1967 1993 1.071 .934 .911 .977 .921 1.437 80 346 .912 .914 100 4120 6790 102 112 259 269 0 1497 252 1246 1.225 1497 1246 .816 1.194 .293 .256
17 645 502 191 192 454 310 632 488 196 202 441 296 0 0 136 133 45 73 100 98 100 90 764 737 1.465 .683 .671 .638 .716 1.886 52 288 .692 .582 90 4260 6790 102 111 273 282 0 658 252 406 .895 640 388 1.117 .88 -.16 -.184
18 780 569 188 204 592 365 762 553 195 212 574 349 0 0 171 126 53 80 100 100 100 98 957 923 1.622 .617 .608 .599 .627 1.501 52 300 .617 .677 90 4410 6790 102 111 288 297 0 746 267 479 .808 725 458 1.237 .797 -.307 -.327
19 1189 917 185 202 1004 715 1123 873 191 207 938 671 0 0 375 329 49 77 98 100 98 97 1719 1609 1.404 .712 .715 .714 .712 1.639 80 377 .739 .841 100 4560 6790 102 112 303 313 0 1202 265 938 .934 1145 880 1.071 .938 -.099 -.092
20 654 375 188 187 466 188 639 368 193 196 451 181 0 0 109 96 43 69 100 92 100 65 654 632 2.479 .403 .401 .373 .407 1.768 52 302 .416 .508 90 4710 6780 101 110 318 327 0 492 245 247 .529 483 237 1.89 .526 -.919 -.926

Total number of rows: 41472

Table truncated, full table size 9268 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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