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Sample GSM148746 Query DataSets for GSM148746
Status Public on Oct 03, 2007
Title PL129_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 53572.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL129_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL129_1 DNA
Prostate genomic DNA; LabeledExtract: 53572.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, 5560; 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 = 39.47; Parameter Scan Time = 11:28:14; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173176; 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 = 39.47; Parameter Scan Time = 11:28:14; Parameter PMT Volts = 680; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537979; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; 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/2004-07/53572.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
1 638 525 222 238 416 287 611 502 224 241 389 264 0 0 186 165 51 60 96 96 94 84 703 653 1.449 .69 .679 .694 .724 1.739 52 268 .689 .675 80 1650 6090 49 57 49 57 0 539 244 295 .709 516 271 1.411 .697 -.497 -.521
2 1003 893 211 231 792 662 1019 885 217 236 808 654 0 0 289 243 47 63 100 100 100 100 1454 1462 1.196 .836 .809 .844 .827 1.39 52 256 .83 .845 80 1790 6090 49 57 63 71 0 917 237 680 .858 909 672 1.165 .831 -.22 -.267
3 653 605 214 237 439 368 636 581 214 244 422 344 0 0 143 194 47 64 100 100 100 90 807 766 1.193 .838 .815 .765 .731 1.662 32 213 .962 .594 70 1930 6090 49 56 77 84 0 621 243 378 .861 597 353 1.162 .837 -.216 -.256
4 879 779 214 240 665 539 838 724 219 240 624 484 0 0 224 216 51 61 100 100 100 100 1204 1108 1.234 .811 .776 .803 .832 1.396 32 210 .85 .806 70 2090 6080 48 55 93 100 0 800 246 554 .832 744 497 1.201 .797 -.265 -.328
5 669 565 215 224 454 341 644 584 222 231 429 360 0 0 158 130 48 63 100 98 100 96 795 789 1.331 .751 .839 .721 .757 1.745 52 276 .733 .688 80 2220 6090 49 57 106 114 0 580 230 350 .771 600 370 1.296 .862 -.375 -.215
6 626 536 211 234 415 302 650 510 220 244 439 276 0 0 219 199 48 63 96 90 96 84 717 715 1.374 .728 .629 .697 .73 3.254 32 170 .74 .665 60 2380 6090 50 56 123 129 0 550 240 310 .747 524 283 1.338 .646 -.42 -.631
7 601 347 209 236 392 111 597 349 218 244 388 113 0 0 115 79 55 63 100 71 100 40 503 501 3.532 .283 .291 .247 .269 2.149 32 220 .294 .374 70 2520 6090 49 56 136 143 0 356 242 114 .291 358 116 3.439 .299 -1.782 -1.741
8 898 787 217 233 681 554 854 745 224 238 637 512 0 0 303 264 44 60 100 100 100 100 1235 1149 1.229 .814 .804 .83 .874 1.512 32 152 .796 .815 60 2670 6090 50 56 152 158 0 808 239 569 .835 765 526 1.197 .825 -.259 -.277
9 920 1300 217 236 703 1064 971 1342 222 242 754 1106 0 0 220 242 46 58 97 100 97 100 1767 1860 .661 1.514 1.467 1.614 1.495 1.556 80 338 1.51 .854 100 2810 6080 47 57 164 174 0 1335 242 1093 1.554 1378 1136 .643 1.506 .636 .591
10 1329 1412 216 240 1113 1172 1489 1478 221 243 1273 1238 0 0 448 341 47 59 98 100 96 100 2285 2511 .95 1.053 .973 1.192 1.036 1.83 80 379 1.029 .906 110 2950 6080 46 57 177 188 0 1450 246 1204 1.081 1518 1271 .925 .999 .113 -.002
11 738 749 216 234 522 515 726 749 219 239 510 515 0 0 140 144 51 63 100 100 100 100 1037 1025 1.014 .987 1.01 .987 1.003 1.396 52 300 1.026 .815 90 3100 6080 47 56 193 202 0 769 240 529 1.013 769 529 .987 1.037 .019 .052
12 871 856 225 248 646 608 803 818 234 254 578 570 0 0 258 186 75 65 100 100 98 100 1254 1148 1.063 .941 .986 .983 .948 1.439 52 313 .872 .843 90 3240 6080 47 56 207 216 0 879 255 624 .967 840 585 1.035 1.013 -.049 .018
13 1035 1168 228 242 807 926 920 1098 235 250 692 856 0 0 407 384 70 65 98 100 97 98 1733 1548 .871 1.147 1.237 1.187 1.209 1.454 80 371 1.091 .873 100 3400 6080 47 57 223 233 0 1200 249 951 1.178 1128 879 .849 1.27 .237 .345
14 1429 1969 218 239 1211 1730 1474 1984 226 243 1256 1745 0 0 255 323 51 63 100 100 100 100 2941 3001 .7 1.429 1.389 1.455 1.419 1.28 80 374 1.434 .925 110 3540 6080 46 57 236 247 0 2022 245 1777 1.467 2038 1792 .682 1.427 .553 .513
15 870 950 220 245 650 705 836 908 227 251 616 663 0 0 407 328 51 66 97 100 97 98 1355 1279 .922 1.085 1.076 1.156 1.114 1.59 80 372 .994 .768 110 3680 6080 46 57 250 261 0 976 252 724 1.114 932 681 .898 1.105 .156 .144
16 4103 4965 231 247 3872 4718 4487 5164 236 256 4256 4917 0 0 1223 958 49 68 100 100 98 100 8590 9173 .821 1.218 1.155 1.345 1.184 1.697 80 381 1.176 .938 110 3830 6080 46 57 265 276 0 5099 254 4845 1.251 5303 5050 .799 1.186 .324 .247
17 1301 1717 236 260 1065 1457 1380 1753 243 266 1144 1493 0 0 413 433 51 70 100 100 96 98 2522 2637 .731 1.368 1.305 1.468 1.338 1.506 80 338 1.331 .901 100 3980 6080 47 57 281 291 0 1763 267 1496 1.405 1800 1533 .712 1.34 .491 .423
18 1697 1821 238 273 1459 1548 1772 1893 243 272 1534 1620 0 0 400 358 48 64 100 100 100 100 3007 3154 .943 1.061 1.056 1.079 1.035 1.351 80 324 1.048 .903 100 4130 6080 47 57 296 306 0 1870 280 1590 1.09 1944 1664 .918 1.085 .124 .117
19 3017 3173 238 267 2779 2906 3108 3280 243 269 2870 3013 0 0 653 565 45 62 100 100 100 100 5685 5883 .956 1.046 1.05 1.063 1.019 1.328 80 312 1.03 .928 100 4270 6080 47 57 310 320 0 3259 274 2984 1.074 3368 3094 .931 1.078 .103 .109
20 1348 994 238 269 1110 725 1346 993 241 278 1108 724 0 0 215 177 46 63 100 100 100 100 1835 1832 1.531 .653 .653 .645 .629 1.396 80 335 .635 .838 100 4410 6080 47 57 324 334 0 1021 276 745 .671 1020 744 1.491 .671 -.576 -.575

Total number of rows: 41472

Table truncated, full table size 9473 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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