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Sample GSM148701 Query DataSets for GSM148701
Status Public on Oct 03, 2007
Title PT316_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48003.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT316_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT316_2 DNA
Prostate genomic DNA; LabeledExtract: 48003.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 = 490, 5320; 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 = 38.74; Parameter Scan Time = 12:05:15; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142669; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; 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 = 38.74; Parameter Scan Time = 12:05:15; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.23; 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/2004-01/48003.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 GPL4640
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
1 850 708 133 154 717 554 840 715 136 157 707 561 0 0 181 150 30 43 100 100 100 100 1271 1268 1.294 .773 .793 .769 .755 1.287 32 225 .782 .862 70 1790 6170 81 88 126 133 0 678 147 530 .74 685 537 1.352 .76 -.435 -.397
2 1204 863 133 150 1071 713 1239 848 140 153 1106 698 0 0 290 344 38 42 100 100 100 100 1784 1804 1.502 .666 .631 .602 .656 1.587 32 170 .691 .797 60 1950 6170 82 88 143 149 0 826 144 683 .637 812 668 1.569 .604 -.65 -.727
3 1553 1701 134 148 1419 1553 1706 1911 137 151 1572 1763 0 0 601 789 33 36 100 100 100 100 2972 3335 .914 1.094 1.122 .995 1.077 1.57 52 297 1.146 .945 80 2090 6170 81 89 156 164 0 1628 142 1487 1.048 1830 1688 .954 1.074 .067 .103
4 1144 675 135 143 1009 532 1269 710 140 144 1134 567 0 0 309 191 32 32 100 100 100 100 1541 1701 1.897 .527 .5 .512 .525 1.492 32 156 .527 .853 60 2250 6180 83 89 173 179 0 646 137 509 .505 680 543 1.981 .479 -.986 -1.063
5 1692 1574 136 152 1556 1422 1815 1631 138 155 1679 1479 0 0 624 592 34 40 100 100 100 100 2978 3158 1.094 .914 .881 .924 .917 1.286 52 322 .913 .957 90 2370 6180 81 90 183 192 0 1507 146 1361 .875 1561 1416 1.143 .843 -.193 -.246
6 1022 693 139 149 883 544 1043 704 139 152 904 555 0 0 229 194 34 36 100 100 100 100 1427 1459 1.623 .616 .614 .605 .61 1.334 32 171 .63 .878 60 2530 6180 83 89 201 207 0 663 143 521 .59 674 531 1.695 .588 -.762 -.767
7 1634 1651 139 147 1495 1504 1648 1634 142 155 1509 1487 0 0 263 322 40 58 100 100 100 100 2999 2996 .994 1.006 .985 1.001 1.018 1.194 32 222 1.043 .924 70 2670 6170 81 88 214 221 0 1581 141 1440 .963 1564 1424 1.038 .943 -.054 -.084
8 1284 1313 136 153 1148 1160 1281 1352 141 156 1145 1199 0 0 496 549 36 44 100 98 100 96 2308 2344 .99 1.01 1.047 .919 1.022 1.792 52 275 1.032 .937 80 2820 6170 81 89 229 237 0 1257 146 1111 .967 1294 1148 1.034 1.003 -.048 .004
9 924 1093 138 155 786 938 968 1209 139 159 830 1054 0 0 353 395 34 42 100 100 100 100 1724 1884 .838 1.193 1.27 1.216 1.197 1.433 52 253 1.183 .906 80 2970 6180 82 90 244 252 0 1046 148 898 1.143 1157 1009 .875 1.216 .192 .282
10 1639 1450 142 150 1497 1300 1598 1506 144 153 1456 1356 0 0 432 452 33 39 100 100 100 100 2797 2812 1.152 .868 .931 .848 .883 1.31 52 266 .889 .933 80 3110 6170 81 89 258 266 0 1388 144 1245 .831 1442 1298 1.203 .892 -.266 -.165
11 996 875 146 157 850 718 1063 930 156 167 917 773 0 0 238 254 68 62 100 100 100 96 1568 1690 1.184 .845 .843 .8 .817 1.478 32 226 .871 .899 70 3260 6160 80 87 273 280 0 838 150 687 .809 890 740 1.237 .807 -.306 -.309
12 1017 1088 139 151 878 937 1105 1186 143 155 966 1035 0 0 367 389 37 43 100 98 100 98 1815 2001 .937 1.067 1.071 1.058 1.078 1.426 52 295 1.06 .945 80 3410 6170 81 89 288 296 0 1042 145 897 1.022 1135 991 .979 1.026 .031 .037
13 1239 1465 139 149 1100 1316 1308 1544 140 151 1169 1395 0 0 321 452 33 38 100 100 100 100 2416 2564 .836 1.196 1.193 1.159 1.218 1.34 52 243 1.227 .94 80 3560 6170 81 89 303 311 0 1403 143 1260 1.145 1478 1336 .873 1.142 .196 .192
14 1555 1541 139 153 1416 1388 1626 1634 142 156 1487 1481 0 0 427 384 34 38 100 100 100 100 2804 2968 1.02 .98 .996 1.006 .977 1.375 52 333 .965 .941 90 3690 6170 80 89 315 324 0 1475 146 1329 .938 1564 1418 1.066 .954 -.092 -.069
15 932 1042 140 154 792 888 952 1041 143 154 812 887 0 0 139 135 33 40 100 100 100 100 1680 1699 .892 1.121 1.092 1.125 1.106 1.192 32 219 1.115 .911 70 3850 6170 81 88 332 339 0 998 147 850 1.073 997 849 .932 1.046 .102 .065
16 2411 3089 140 152 2271 2937 1877 2441 144 154 1737 2289 0 0 1631 1976 37 52 100 100 100 98 5208 4026 .773 1.293 1.318 1.291 1.261 1.553 52 297 1.271 .942 80 4000 6170 81 89 347 355 0 2957 146 2812 1.238 2337 2191 .808 1.262 .308 .335
17 1278 1445 145 154 1133 1291 1339 1415 146 157 1194 1261 0 0 392 473 34 42 100 100 100 100 2424 2455 .878 1.139 1.056 1.139 1.138 1.212 32 207 1.155 .941 70 4140 6170 81 88 361 368 0 1383 147 1236 1.091 1355 1207 .917 1.011 .125 .016
18 1393 1282 146 147 1247 1135 1380 1296 146 151 1234 1149 0 0 421 441 32 38 100 100 100 100 2382 2383 1.099 .91 .931 .884 .908 1.336 52 265 .921 .935 80 4290 6170 81 89 376 384 0 1227 141 1087 .871 1241 1100 1.148 .891 -.199 -.166
19 2996 3141 140 154 2856 2987 3016 3198 146 160 2876 3044 0 0 741 821 36 52 100 100 100 100 5843 5920 .956 1.046 1.058 1.042 1.024 1.244 52 312 1.058 .94 90 4430 6170 80 89 389 398 0 3007 147 2860 1.001 3062 2914 .999 1.013 .002 .019
20 1009 812 141 153 868 659 1012 815 144 157 871 662 0 0 241 235 35 36 100 100 100 100 1527 1533 1.317 .759 .76 .724 .733 1.398 52 274 .769 .901 80 4570 6170 81 89 404 412 0 777 146 631 .727 780 634 1.376 .728 -.46 -.459

Total number of rows: 41664

Table truncated, full table size 9699 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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