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Sample GSM148742 Query DataSets for GSM148742
Status Public on Oct 03, 2007
Title PL27_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 53424.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL27_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL27_1 DNA
Prostate genomic DNA; LabeledExtract: 53424.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 = 39.71; Parameter Scan Time = 11:29:46; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 172596; 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 = 39.71; Parameter Scan Time = 11:29:46; Parameter PMT Volts = 750; Parameter Scan Date = 2004-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 537400; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; 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/2004-07/53424.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
1 574 432 202 283 372 149 562 432 207 291 360 149 0 0 140 128 42 91 98 69 94 36 521 509 2.497 .401 .414 .392 .449 3.05 52 278 .452 .219 80 1760 6480 96 104 60 68 0 482 316 166 .447 482 166 2.238 .462 -1.162 -1.115
2 832 679 208 294 624 385 800 694 205 301 592 400 0 0 149 177 41 93 100 98 100 82 1009 992 1.621 .617 .676 .546 .635 1.8 52 264 .659 .644 80 1910 6480 96 104 75 83 0 757 328 429 .688 774 446 1.453 .754 -.539 -.408
3 591 506 209 274 382 232 576 511 208 287 367 237 0 0 115 128 42 99 100 80 100 59 614 604 1.647 .607 .646 .484 .591 2.569 52 254 .713 .404 80 2060 6480 96 104 90 98 0 564 306 259 .677 570 264 1.476 .72 -.562 -.473
4 594 517 209 292 385 225 587 488 212 295 378 196 0 0 133 191 47 93 100 73 100 51 610 574 1.711 .584 .519 .516 .592 2.001 52 254 .806 .449 80 2200 6480 96 104 104 112 0 577 326 251 .652 544 219 1.534 .578 -.617 -.79
5 570 505 207 293 363 212 577 492 211 292 370 199 0 0 72 134 45 87 100 86 100 57 575 569 1.712 .584 .538 .541 .628 2.013 52 275 .78 .402 80 2350 6470 95 103 119 127 0 563 327 236 .651 549 222 1.535 .6 -.618 -.737
6 580 591 211 289 369 302 561 588 216 295 350 299 0 0 111 156 42 88 100 90 100 78 671 649 1.222 .818 .854 .814 .923 1.68 32 207 1.033 .447 70 2500 6480 96 103 134 141 0 659 322 337 .913 656 334 1.095 .953 -.131 -.07
7 500 413 207 288 293 125 510 405 214 299 303 117 0 0 105 118 49 92 98 57 94 26 418 420 2.344 .427 .386 .379 .473 3.038 52 265 .495 .184 80 2640 6480 96 104 148 156 0 461 321 139 .476 452 131 2.101 .431 -1.071 -1.215
8 714 592 214 293 500 299 735 592 215 298 521 299 0 0 136 168 49 92 100 84 100 75 799 820 1.672 .598 .574 .538 .603 1.704 32 199 .701 .587 70 2790 6470 95 102 163 170 0 660 327 334 .667 660 334 1.499 .64 -.584 -.643
9 674 696 210 294 464 402 660 673 211 304 450 379 0 0 121 194 46 99 100 96 100 85 866 829 1.154 .866 .842 .804 .862 1.554 80 339 .984 .709 100 2930 6470 94 104 176 186 0 776 328 448 .966 751 423 1.035 .939 -.049 -.09
10 841 638 214 293 627 345 844 627 218 302 630 334 0 0 186 177 46 97 100 90 100 80 972 964 1.817 .55 .53 .485 .546 1.938 80 296 .552 .56 100 3070 6480 95 105 190 200 0 712 327 385 .614 699 373 1.629 .591 -.704 -.758
11 586 513 214 282 372 231 592 504 218 288 378 222 0 0 111 137 46 92 100 83 100 62 603 600 1.61 .621 .587 .581 .626 1.79 80 384 .804 .5 110 3220 6470 93 104 204 215 0 572 315 258 .693 562 248 1.444 .655 -.53 -.61
12 871 777 211 284 660 493 869 787 216 296 658 503 0 0 166 193 44 96 100 97 100 95 1153 1161 1.339 .747 .764 .701 .736 1.484 80 354 .803 .757 100 3370 6470 94 104 220 230 0 867 317 550 .833 878 561 1.2 .853 -.263 -.23
13 1223 1151 211 281 1012 870 1233 1159 215 296 1022 878 0 0 185 301 44 100 100 97 100 97 1882 1900 1.163 .86 .859 .788 .863 1.673 80 323 .919 .836 100 3520 6470 94 104 235 245 0 1284 313 970 .959 1293 979 1.043 .958 -.06 -.061
14 1354 1634 213 290 1141 1344 1369 1661 216 289 1156 1371 0 0 222 306 45 96 100 100 100 100 2485 2527 .849 1.178 1.186 1.167 1.167 1.278 80 362 1.232 .898 110 3660 6470 93 104 248 259 0 1823 323 1499 1.314 1853 1529 .761 1.323 .394 .404
15 742 815 208 272 534 543 742 812 211 283 534 540 0 0 116 167 45 94 100 100 100 100 1077 1074 .983 1.017 1.011 .989 1.016 1.412 80 371 1.076 .77 110 3810 6470 93 104 263 274 0 909 303 606 1.134 906 602 .882 1.128 .182 .174
16 4676 4729 210 278 4466 4451 4736 4746 215 287 4526 4468 0 0 937 822 50 98 100 100 100 100 8917 8994 1.003 .997 .987 1.006 .976 1.175 80 374 .985 .969 110 3950 6470 93 104 277 288 0 5275 310 4965 1.112 5294 4984 .899 1.101 .153 .139
17 1526 1404 213 285 1313 1119 1540 1393 219 300 1327 1108 0 0 186 265 47 96 100 100 100 100 2432 2435 1.173 .852 .835 .837 .846 1.28 80 338 .873 .883 100 4100 6470 94 104 293 303 0 1566 318 1248 .951 1554 1236 1.052 .931 -.073 -.103
18 1928 1836 211 288 1717 1548 1966 1872 215 301 1755 1584 0 0 324 397 48 93 100 100 100 100 3265 3339 1.109 .902 .903 .883 .932 1.295 80 313 .921 .916 100 4250 6470 94 104 308 318 0 2048 321 1727 1.006 2088 1767 .994 1.007 .008 .01
19 3101 3443 211 284 2890 3159 3135 3452 215 293 2924 3168 0 0 529 682 45 94 100 100 100 100 6049 6092 .915 1.093 1.083 1.086 1.076 1.18 80 344 1.102 .95 110 4390 6470 93 104 321 332 0 3841 317 3524 1.219 3851 3534 .82 1.209 .286 .273
20 1308 1059 220 284 1088 775 1317 1045 220 297 1097 761 0 0 216 225 44 96 100 100 100 100 1863 1858 1.404 .712 .694 .696 .694 1.3 80 326 .738 .868 100 4540 6470 94 104 337 347 0 1181 317 864 .795 1166 849 1.259 .774 -.332 -.37

Total number of rows: 41472

Table truncated, full table size 9488 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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