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Sample GSM148756 Query DataSets for GSM148756
Status Public on Oct 03, 2007
Title PL115_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49669.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL115_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL115_2 DNA
Prostate genomic DNA; LabeledExtract: 49669.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 = 1080, 5200; 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 = 38.79; Parameter Scan Time = 10:53:30; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148345; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; 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 = 38.79; Parameter Scan Time = 10:53:30; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513249; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; 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/2004-02/49669.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 GPL4640
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
1 421 420 117 138 304 282 423 426 120 140 306 288 0 0 129 147 34 42 98 98 96 86 586 594 1.078 .928 .941 .916 .954 1.582 52 301 .977 .742 80 1820 6280 104 112 70 78 0 506 166 340 1.117 513 347 .895 1.133 .159 .18
2 688 707 116 144 572 563 700 724 117 145 584 580 0 0 109 191 28 39 100 100 100 100 1135 1164 1.016 .984 .993 .927 1.014 1.549 32 204 1.087 .794 70 1950 6280 104 111 83 90 0 851 173 678 1.185 872 698 .844 1.196 .245 .258
3 814 1011 115 152 699 859 902 1056 117 153 787 904 0 0 316 279 29 42 100 100 92 100 1558 1691 .814 1.229 1.149 1.438 1.215 1.978 52 337 1.145 .828 90 2090 6290 104 113 96 105 0 1217 183 1034 1.48 1271 1088 .676 1.383 .565 .468
4 596 486 118 143 478 343 589 506 121 146 471 363 0 0 91 135 33 48 100 100 100 100 821 834 1.394 .718 .771 .66 .734 1.612 32 225 .766 .711 70 2240 6280 104 111 112 119 0 585 172 413 .864 609 437 1.157 .928 -.211 -.108
5 1018 746 116 137 902 609 1008 806 119 140 892 669 0 0 219 233 31 40 100 98 100 92 1511 1561 1.481 .675 .75 .595 .684 1.959 52 344 .711 .809 90 2390 6280 103 112 126 135 0 898 165 733 .813 970 805 1.23 .903 -.299 -.147
6 470 501 117 144 353 357 467 486 121 145 350 342 0 0 69 124 29 42 100 100 100 100 710 692 .989 1.011 .977 .969 1.045 1.432 32 170 1.097 .698 60 2530 6280 105 111 142 148 0 603 173 430 1.218 585 412 .821 1.177 .284 .235
7 696 672 117 138 579 534 690 691 121 141 573 553 0 0 149 235 29 41 100 92 100 92 1113 1126 1.084 .922 .965 .823 .963 2.049 52 285 1.018 .813 80 2680 6280 104 112 156 164 0 809 166 643 1.11 832 666 .901 1.162 .151 .217
8 774 536 115 142 659 394 702 514 118 146 587 372 0 0 276 264 30 46 100 96 100 94 1053 959 1.673 .598 .634 .526 .561 1.808 52 304 .637 .755 90 2820 6280 103 112 169 178 0 645 171 474 .72 619 448 1.389 .763 -.474 -.39
9 506 601 121 146 385 455 475 600 125 150 354 454 0 0 109 142 33 47 100 100 100 100 840 808 .846 1.182 1.282 1.162 1.137 1.453 52 254 1.248 .772 80 2970 6280 104 112 185 193 0 724 176 548 1.423 722 547 .703 1.544 .509 .627
10 815 600 126 152 689 448 773 608 130 156 647 456 0 0 386 250 30 50 100 97 100 92 1137 1103 1.538 .65 .705 .641 .663 1.671 80 359 .617 .827 100 3120 6280 103 113 199 209 0 722 183 539 .783 732 549 1.277 .849 -.353 -.237
11 483 389 128 161 355 228 507 392 129 164 379 231 0 0 129 99 29 45 98 98 98 92 583 610 1.557 .642 .609 .628 .604 2.03 52 254 .587 .555 80 3260 6280 104 112 214 222 0 468 194 275 .773 472 278 1.293 .734 -.371 -.446
12 623 714 122 143 501 571 630 757 125 148 508 614 0 0 143 196 29 43 100 100 100 100 1072 1122 .877 1.14 1.209 1.099 1.17 1.501 52 284 1.187 .855 80 3410 6280 104 112 229 237 0 860 172 687 1.372 911 739 .729 1.455 .457 .541
13 691 766 121 143 570 623 705 808 125 148 584 665 0 0 124 194 29 42 100 98 100 98 1193 1249 .915 1.093 1.139 1.028 1.08 1.657 52 254 1.155 .811 80 3560 6280 104 112 244 252 0 922 172 750 1.316 973 801 .76 1.371 .396 .455
14 705 770 121 143 584 627 774 849 122 147 653 706 0 0 253 318 29 41 100 95 96 93 1211 1359 .931 1.074 1.081 .968 1.076 2.421 80 368 1.125 .839 100 3710 6280 103 113 258 268 0 927 172 755 1.293 1022 850 .774 1.302 .37 .38
15 470 392 118 138 352 254 484 395 121 143 366 257 0 0 88 76 31 43 100 100 100 98 606 623 1.386 .722 .702 .708 .7 1.513 52 288 .694 .63 90 3850 6280 103 112 272 281 0 472 166 306 .869 476 309 1.151 .845 -.203 -.242
16 1687 2007 125 135 1562 1872 1719 2016 126 141 1594 1881 0 0 390 486 31 44 100 100 100 100 3434 3475 .834 1.198 1.18 1.195 1.24 1.327 52 276 1.212 .889 80 4000 6280 104 112 288 296 0 2416 163 2254 1.443 2427 2265 .693 1.421 .529 .507
17 717 793 119 141 598 652 710 795 120 148 591 654 0 0 184 272 29 46 100 100 100 98 1250 1245 .917 1.09 1.107 1.012 1.119 1.606 52 252 1.144 .823 80 4150 6280 104 112 303 311 0 955 170 785 1.313 957 787 .762 1.332 .393 .414
18 883 1031 121 139 762 892 922 1082 126 145 801 943 0 0 152 247 50 44 100 100 100 100 1654 1744 .854 1.171 1.177 1.141 1.171 1.319 52 267 1.206 .849 80 4300 6280 104 112 318 326 0 1241 167 1074 1.409 1303 1135 .71 1.417 .495 .503
19 2302 2263 122 142 2180 2121 2294 2352 124 145 2172 2210 0 0 506 841 31 44 100 100 100 100 4301 4382 1.028 .973 1.017 .829 1.058 2.284 52 317 1.03 .822 90 4440 6270 102 111 331 340 0 2725 171 2554 1.171 2832 2661 .854 1.225 .228 .293
20 785 446 121 146 664 300 793 463 122 150 672 317 0 0 137 122 28 40 100 96 100 92 964 989 2.213 .452 .472 .405 .437 1.721 52 345 .453 .73 90 4590 6270 102 111 346 355 0 537 176 361 .544 557 382 1.838 .568 -.878 -.816

Total number of rows: 41664

Table truncated, full table size 9357 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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