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Sample GSM148745 Query DataSets for GSM148745
Status Public on Oct 03, 2007
Title PL122_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 53571.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL122_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL122_1 DNA
Prostate genomic DNA; LabeledExtract: 53571.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 = 1120, 5480; 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 = 38.99; Parameter Scan Time = 10:30:49; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173117; 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 = 38.99; Parameter Scan Time = 10:30:49; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537921; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.94; 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/2004-07/53571.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
1 696 240 174 172 522 68 700 242 177 177 526 70 0 0 128 71 42 47 100 59 100 36 590 596 7.676 .13 .133 .133 .154 2.185 52 278 .102 .133 80 1680 6210 69 77 52 60 0 262 188 74 .142 264 76 7.04 .145 -2.816 -2.785
2 917 764 181 180 736 584 909 765 181 187 728 585 0 0 213 164 41 52 100 100 100 100 1320 1313 1.26 .793 .804 .799 .784 1.281 52 254 .778 .902 80 1820 6210 69 77 66 74 0 833 196 637 .865 834 638 1.156 .876 -.209 -.191
3 582 442 183 175 399 267 589 442 185 182 406 267 0 0 162 123 42 53 98 96 98 90 666 673 1.494 .669 .658 .66 .686 1.891 52 272 .647 .7 80 1960 6210 69 77 80 88 0 482 191 291 .73 482 291 1.37 .717 -.455 -.48
4 671 555 185 187 486 368 654 549 185 190 469 362 0 0 146 131 41 52 100 98 100 94 854 831 1.321 .757 .772 .727 .742 1.357 52 260 .763 .838 80 2120 6210 69 77 96 104 0 605 204 401 .826 599 395 1.211 .842 -.276 -.249
5 541 391 188 185 353 206 523 381 193 191 335 196 0 0 93 96 51 58 100 98 100 80 559 531 1.714 .584 .585 .54 .557 1.676 52 260 .574 .564 80 2250 6210 69 77 109 117 0 426 202 225 .636 415 214 1.571 .638 -.652 -.648
6 569 474 183 187 386 287 564 446 191 196 381 259 0 0 106 129 54 66 100 96 100 90 673 640 1.345 .744 .68 .664 .759 1.728 32 170 .803 .692 60 2410 6210 70 76 126 132 0 517 204 313 .811 486 282 1.233 .741 -.303 -.432
7 536 274 195 203 341 71 537 267 194 208 342 64 0 0 86 69 45 55 100 56 100 28 412 406 4.803 .208 .187 .218 .223 2.47 32 214 .187 .175 70 2550 6210 69 76 139 146 0 299 221 77 .227 291 70 4.405 .204 -2.139 -2.293
8 662 504 193 191 469 313 670 511 195 195 477 320 0 0 201 167 41 48 98 94 92 88 782 797 1.498 .667 .671 .638 .683 1.707 52 252 .673 .787 80 2700 6210 69 77 154 162 0 550 208 341 .728 557 349 1.374 .732 -.459 -.451
9 569 414 190 188 379 226 550 398 195 197 360 210 0 0 116 88 45 52 100 98 100 95 605 570 1.677 .596 .583 .579 .584 1.527 80 333 .584 .632 100 2840 6210 68 78 167 177 0 451 205 246 .65 434 229 1.538 .636 -.621 -.653
10 820 922 195 200 625 722 768 895 200 204 573 695 0 0 218 226 49 51 100 100 100 100 1347 1268 .866 1.155 1.213 1.169 1.157 1.315 80 326 1.148 .886 100 2990 6210 68 78 182 192 0 1005 218 787 1.26 976 758 .794 1.323 .333 .403
11 636 537 201 199 435 338 621 522 206 203 420 323 0 0 118 102 51 50 100 100 100 100 773 743 1.287 .777 .769 .773 .804 1.449 52 310 .74 .73 90 3130 6200 67 76 196 205 0 586 217 369 .847 569 352 1.18 .839 -.239 -.254
12 856 618 208 196 648 422 834 626 209 201 626 430 0 0 200 130 49 50 100 100 100 100 1070 1056 1.536 .651 .687 .653 .676 1.312 52 289 .637 .815 90 3280 6210 68 77 211 220 0 674 214 460 .71 683 469 1.408 .749 -.494 -.417
13 790 596 200 209 590 387 807 591 204 236 607 382 0 0 177 125 47 203 98 90 98 42 977 989 1.525 .656 .629 .668 .675 1.593 80 345 .68 .655 100 3420 6210 68 78 225 235 0 650 228 422 .715 644 417 1.398 .686 -.483 -.543
14 1101 1075 204 209 897 866 1118 1082 208 219 914 873 0 0 156 153 45 76 100 100 100 100 1763 1787 1.036 .965 .955 .964 .971 1.222 80 360 .965 .898 110 3570 6210 67 78 239 250 0 1172 228 944 1.053 1180 952 .95 1.042 .074 .059
15 569 478 218 228 351 250 579 469 218 234 361 241 0 0 81 87 47 56 100 100 100 97 601 602 1.404 .712 .668 .686 .691 1.516 80 322 .7 .67 100 3710 6210 68 78 254 264 0 521 249 273 .777 511 263 1.288 .728 -.365 -.458
16 2826 2801 221 238 2605 2563 2929 2900 220 242 2708 2662 0 0 609 623 51 57 100 100 100 100 5168 5370 1.016 .984 .983 .979 .978 1.222 80 334 .986 .929 100 3860 6210 68 78 269 279 0 3054 260 2795 1.073 3162 2903 .932 1.072 .101 .1
17 948 801 215 232 733 569 997 814 221 233 782 582 0 0 276 164 52 54 96 100 95 98 1302 1364 1.288 .776 .744 .851 .764 1.897 80 342 .743 .84 100 4010 6200 67 77 284 294 0 873 253 620 .846 888 635 1.181 .812 -.24 -.301
18 1088 800 209 232 879 568 1156 804 215 234 947 572 0 0 235 148 47 54 100 100 100 100 1447 1519 1.548 .646 .604 .659 .643 1.419 80 342 .624 .857 100 4160 6200 67 77 299 309 0 872 253 619 .705 877 624 1.419 .659 -.505 -.602
19 2071 1926 221 239 1850 1687 2110 1957 226 244 1889 1718 0 0 357 326 50 57 100 100 100 100 3537 3607 1.097 .912 .909 .913 .903 1.204 80 313 .915 .909 100 4300 6210 68 78 313 323 0 2100 261 1840 .994 2134 1873 1.006 .992 -.008 -.012
20 817 526 233 243 584 283 832 516 238 248 599 273 0 0 135 97 54 59 100 100 100 97 867 872 2.064 .485 .456 .47 .456 1.507 80 323 .471 .666 100 4440 6210 68 78 327 337 0 574 265 309 .528 563 298 1.892 .497 -.92 -1.009

Total number of rows: 41472

Table truncated, full table size 9417 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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