NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148743 Query DataSets for GSM148743
Status Public on Oct 03, 2007
Title PL118_3.2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 53570.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL118_3.2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL118_3.2 DNA
Prostate genomic DNA; LabeledExtract: 53570.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 = 1360, 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 = 38.67; Parameter Scan Time = 10:07:36; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173094; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; 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 = 38.67; Parameter Scan Time = 10:07:36; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537898; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; 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/2004-07/53570.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
1 488 237 166 183 322 54 484 235 171 184 318 52 0 0 88 79 44 47 100 50 100 25 376 370 5.963 .168 .164 .193 .219 2.465 52 286 .195 .161 80 1710 6260 74 82 31 39 0 255 197 58 .18 253 56 5.541 .176 -2.47 -2.506
2 646 432 169 172 477 260 657 421 170 178 488 249 0 0 161 152 43 52 100 92 98 88 737 737 1.835 .545 .51 .466 .509 2.038 52 244 .568 .665 80 1850 6260 74 82 45 53 0 465 185 280 .587 453 268 1.705 .549 -.77 -.865
3 428 259 170 164 258 95 422 232 175 168 252 68 0 0 72 94 42 48 100 63 100 44 353 320 2.716 .368 .27 .341 .407 2.388 52 264 .421 .245 80 1990 6260 74 82 59 67 0 279 176 102 .396 250 73 2.523 .29 -1.335 -1.784
4 489 280 170 165 319 115 496 272 186 172 326 107 0 0 119 98 195 47 82 71 23 55 434 433 2.774 .361 .328 .293 .33 2.651 52 264 .367 .355 80 2140 6260 74 82 74 82 0 301 178 124 .388 293 115 2.577 .353 -1.366 -1.501
5 424 250 168 163 256 87 425 244 168 164 257 81 0 0 84 61 39 47 100 73 100 38 343 338 2.943 .34 .315 .314 .353 2.01 52 321 .312 .272 90 2280 6260 73 82 87 96 0 269 175 94 .366 263 87 2.734 .339 -1.451 -1.56
6 488 285 163 163 325 122 483 269 171 168 320 106 0 0 84 100 58 61 100 65 100 46 447 426 2.664 .375 .331 .341 .429 2.268 32 220 .413 .323 70 2440 6260 74 81 104 111 0 307 175 131 .404 290 114 2.475 .356 -1.308 -1.488
7 512 238 166 166 346 72 509 234 171 170 343 68 0 0 71 70 41 48 100 62 100 34 418 411 4.806 .208 .198 .2 .237 2.369 32 216 .173 .173 70 2580 6260 74 81 118 125 0 256 179 77 .224 252 73 4.465 .213 -2.159 -2.229
8 697 432 171 184 526 248 678 405 179 187 507 221 0 0 136 103 47 47 100 100 100 96 774 728 2.121 .471 .436 .447 .445 1.5 32 215 .449 .673 70 2720 6250 73 80 132 139 0 465 198 267 .507 436 238 1.971 .469 -.979 -1.092
9 650 635 175 182 475 453 651 652 184 186 476 470 0 0 111 128 49 51 100 98 100 98 928 946 1.049 .954 .987 .927 .959 1.583 80 349 .981 .764 100 2870 6260 73 83 146 156 0 683 196 488 1.026 702 506 .974 1.063 .038 .088
10 971 583 178 186 793 397 980 579 180 186 802 393 0 0 195 122 42 47 100 100 100 98 1190 1195 1.997 .501 .49 .489 .494 1.392 80 343 .484 .799 110 3010 6260 72 83 159 170 0 627 200 427 .539 623 423 1.856 .527 -.892 -.923
11 546 460 180 186 366 274 542 452 182 189 362 266 0 0 101 104 42 51 98 97 98 92 640 628 1.336 .749 .735 .695 .744 1.944 80 338 .737 .658 100 3160 6260 73 83 175 185 0 495 200 295 .806 486 286 1.241 .791 -.312 -.339
12 676 699 189 189 487 510 680 684 189 191 491 495 0 0 96 111 45 56 100 100 100 100 997 986 .955 1.047 1.008 1.043 1.067 1.327 52 290 1.025 .806 90 3300 6250 72 81 189 198 0 752 203 549 1.127 736 533 .887 1.085 .173 .118
13 809 782 190 201 619 581 797 798 194 203 607 597 0 0 134 179 45 55 100 100 100 100 1200 1204 1.065 .939 .984 .908 .934 1.403 80 345 .969 .845 100 3450 6260 73 83 204 214 0 842 216 625 1.01 859 643 .99 1.058 .015 .082
14 881 907 193 189 688 718 838 898 198 195 645 709 0 0 174 211 50 56 100 100 100 100 1406 1354 .958 1.044 1.099 1.032 1.026 1.295 80 353 1.035 .87 110 3600 6260 72 83 218 229 0 976 203 773 1.123 966 763 .89 1.183 .168 .242
15 545 518 194 194 351 324 547 501 201 198 353 307 0 0 128 109 50 54 100 100 98 98 675 660 1.083 .923 .87 .942 .924 1.537 80 307 .931 .711 100 3740 6260 73 83 233 243 0 557 209 349 .993 539 330 1.007 .936 -.01 -.095
16 2685 2970 194 202 2491 2768 2762 3187 202 209 2568 2985 0 0 415 699 48 52 100 100 100 100 5259 5553 .9 1.111 1.162 1.074 1.137 1.311 80 319 1.137 .945 100 3890 6260 73 83 248 258 0 3196 217 2979 1.196 3430 3213 .836 1.251 .258 .323
17 883 848 201 209 682 639 913 909 209 211 712 700 0 0 173 221 50 52 98 97 97 97 1321 1412 1.067 .937 .983 .902 .964 1.41 80 316 .978 .884 100 4040 6260 73 83 263 273 0 913 225 688 1.008 978 753 .992 1.058 .012 .081
18 1030 1052 205 218 825 834 1037 1081 210 222 832 863 0 0 178 209 51 56 100 100 100 100 1659 1695 .989 1.011 1.037 1.002 1.029 1.32 80 326 1.018 .873 100 4190 6250 72 82 278 288 0 1132 235 898 1.088 1163 929 .919 1.116 .122 .159
19 1877 1937 201 219 1676 1718 1880 2065 207 224 1679 1846 0 0 382 516 51 59 100 100 100 100 3394 3525 .976 1.025 1.099 .991 1.082 1.357 80 331 1.048 .92 110 4330 6260 72 83 291 302 0 2085 236 1849 1.103 2222 1987 .906 1.183 .142 .243
20 802 635 209 217 593 418 789 628 214 219 580 411 0 0 126 130 50 61 100 97 100 97 1011 991 1.419 .705 .709 .668 .688 1.571 80 335 .7 .735 100 4470 6250 72 82 306 316 0 683 234 450 .759 676 442 1.318 .763 -.399 -.391

Total number of rows: 41472

Table truncated, full table size 9428 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap