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Sample GSM148747 Query DataSets for GSM148747
Status Public on Oct 03, 2007
Title PL194_3 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 53573.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL194_3 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL194_3 DNA
Prostate genomic DNA; LabeledExtract: 53573.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, 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 = 39.31; Parameter Scan Time = 11:08:56; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173155; 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 = 39.31; Parameter Scan Time = 11:08:56; Parameter PMT Volts = 710; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; 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/2004-07/53573.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
1 487 481 212 266 275 215 467 451 212 267 255 185 0 0 103 142 48 74 100 86 98 63 490 440 1.279 .782 .725 .706 .763 1.976 52 290 1.024 .473 80 1770 6400 64 72 61 69 0 454 251 203 .738 426 175 1.355 .685 -.438 -.546
2 764 897 215 272 549 625 767 928 220 279 552 656 0 0 113 152 56 81 100 100 100 100 1174 1208 .878 1.138 1.188 1.128 1.15 1.37 32 218 1.181 .758 70 1910 6400 64 71 75 82 0 847 257 590 1.075 876 619 .931 1.122 .104 .166
3 580 541 204 277 376 264 558 498 211 279 354 221 0 0 146 195 46 84 100 84 100 59 640 575 1.424 .702 .624 .621 .633 1.897 32 220 .888 .459 70 2060 6410 65 72 90 97 0 511 261 249 .663 470 209 1.509 .589 -.593 -.763
4 591 520 201 262 390 258 572 559 209 271 371 297 0 0 124 145 49 83 100 84 100 71 648 668 1.512 .662 .801 .593 .716 1.808 32 222 .769 .532 70 2200 6400 64 71 104 111 0 491 247 244 .624 528 280 1.601 .756 -.679 -.404
5 487 437 216 270 271 167 482 419 892 596 266 149 0 0 122 108 5401 2725 0 0 0 0 438 415 1.623 .616 .56 .561 .615 2.423 52 274 .605 .306 80 2350 6410 65 73 119 127 0 413 255 158 .582 396 141 1.719 .529 -.782 -.919
6 531 449 206 247 325 202 518 411 209 258 312 164 0 0 105 161 46 73 100 84 100 62 527 476 1.609 .622 .526 .538 .58 1.999 32 170 .75 .403 60 2500 6400 65 71 135 141 0 424 233 191 .587 388 155 1.704 .496 -.769 -1.011
7 486 317 198 261 288 56 501 311 203 265 303 50 0 0 74 84 45 70 100 37 100 12 344 353 5.143 .194 .165 .209 .256 2.756 32 170 .277 .092 60 2650 6400 65 71 150 156 0 299 246 53 .184 294 47 5.448 .156 -2.446 -2.683
8 649 666 202 256 447 410 583 604 205 265 381 348 0 0 301 376 49 79 100 94 100 82 857 729 1.09 .917 .913 .814 .952 1.85 52 244 1.08 .563 80 2790 6400 64 72 163 171 0 629 242 387 .866 570 328 1.155 .862 -.208 -.214
9 621 895 202 263 419 632 625 895 217 275 423 632 0 0 139 197 96 94 95 100 95 98 1051 1055 .663 1.508 1.494 1.55 1.512 1.55 80 332 1.593 .762 100 2930 6400 63 73 176 186 0 845 248 597 1.424 845 597 .702 1.41 .51 .496
10 2815 1302 204 270 2611 1032 949 1269 227 291 745 999 0 0 7970 492 139 165 98 100 98 97 3643 1744 2.53 .395 1.341 1.018 1.222 2.244 80 324 .063 .273 100 3080 6400 63 73 191 201 -100 1229 255 974 .373 1198 943 2.68 1.266 -1.422 .34
11 485 547 205 265 280 282 479 536 220 277 274 271 0 0 101 127 119 156 96 85 71 40 562 545 .993 1.007 .989 .912 1.019 2.248 80 331 1.153 .585 100 3230 6400 63 73 206 216 0 516 250 266 .951 506 256 1.052 .934 -.073 -.099
12 580 809 196 246 384 563 590 823 199 250 394 577 0 0 178 223 47 72 93 98 90 96 947 971 .682 1.466 1.464 1.558 1.453 1.654 80 331 1.465 .817 100 3370 6400 63 73 220 230 0 764 232 531 1.384 777 545 .723 1.382 .469 .467
13 709 889 187 241 522 648 714 911 193 250 527 670 0 0 161 204 53 92 100 97 100 97 1170 1197 .806 1.241 1.271 1.239 1.224 1.425 80 328 1.282 .846 100 3520 6400 63 73 235 245 0 839 227 612 1.172 860 632 .853 1.2 .229 .263
14 955 1252 187 242 768 1010 983 1227 194 252 796 985 0 0 193 243 52 93 100 100 100 100 1778 1781 .76 1.315 1.237 1.334 1.26 1.354 80 319 1.335 .874 100 3660 6400 63 73 249 259 0 1182 228 953 1.241 1158 930 .806 1.168 .312 .224
15 516 616 188 242 328 374 490 594 192 249 302 352 0 0 127 147 44 69 100 100 97 95 702 654 .877 1.14 1.166 1.128 1.092 1.567 80 320 1.22 .687 100 3810 6400 63 73 264 274 0 581 228 353 1.076 561 332 .929 1.1 .106 .138
16 2157 3104 189 242 1968 2862 1865 2605 192 250 1676 2363 0 0 785 1171 45 71 100 100 100 100 4830 4039 .688 1.454 1.41 1.453 1.434 1.233 80 330 1.468 .95 100 3960 6400 63 73 279 289 0 2930 228 2702 1.373 2459 2231 .728 1.331 .457 .412
17 910 1137 194 258 716 879 868 1095 198 257 674 837 0 0 294 324 44 78 100 100 100 100 1595 1511 .815 1.228 1.242 1.249 1.173 1.384 52 277 1.245 .871 90 4100 6390 62 71 293 302 0 1073 244 830 1.159 1034 790 .863 1.172 .213 .229
18 1302 1204 196 262 1106 942 1397 1285 196 259 1201 1023 0 0 359 283 43 74 100 100 100 100 2048 2224 1.174 .852 .852 .882 .868 1.483 80 312 .838 .882 100 4250 6400 63 73 308 318 0 1137 247 889 .804 1213 966 1.244 .804 -.315 -.315
19 2225 3001 185 236 2040 2765 2308 3093 188 246 2123 2857 0 0 627 668 44 72 100 100 97 100 4805 4980 .738 1.355 1.346 1.451 1.368 1.49 80 305 1.324 .946 100 4390 6400 63 73 322 332 0 2833 223 2610 1.279 2920 2697 .782 1.27 .355 .345
20 1069 832 193 242 876 590 1088 824 197 250 895 582 0 0 196 144 45 68 100 100 100 100 1466 1477 1.485 .674 .65 .671 .687 1.387 80 327 .666 .814 100 4540 6400 63 73 337 347 0 785 228 557 .636 778 549 1.573 .614 -.653 -.704

Total number of rows: 41472

Table truncated, full table size 9496 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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