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Sample GSM148716 Query DataSets for GSM148716
Status Public on Oct 03, 2007
Title PT103_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52828.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT103_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT103_1 DNA
Prostate genomic DNA; LabeledExtract: 52828.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 = 1280, 5080; 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 = 38.36; Parameter Scan Time = 09:41:17; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167349; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; 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 = 38.36; Parameter Scan Time = 09:41:17; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532252; 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/2004-06/52828.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
1 591 703 174 201 417 502 576 680 174 204 402 479 0 0 333 206 38 53 100 100 92 100 919 881 .831 1.204 1.192 1.356 1.311 1.676 52 289 .962 .679 80 1790 6290 117 125 47 55 0 562 161 402 .963 544 383 1.038 .953 -.054 -.069
2 1003 1235 180 228 823 1007 1011 1312 216 253 831 1084 0 0 180 237 346 272 100 100 78 93 1830 1915 .817 1.224 1.304 1.215 1.253 1.255 32 219 1.225 .9 70 1930 6280 116 123 61 68 0 988 182 806 .979 1050 867 1.022 1.044 -.031 .062
3 628 846 179 210 449 636 621 843 190 213 442 633 0 0 105 183 62 48 100 100 100 100 1085 1075 .706 1.416 1.432 1.384 1.476 1.397 32 225 1.52 .816 70 2080 6280 116 123 76 83 0 677 168 509 1.133 674 506 .882 1.146 .18 .196
4 812 936 179 205 633 731 670 814 186 209 491 609 0 0 949 506 56 50 100 100 92 100 1364 1100 .866 1.155 1.24 1.376 1.309 1.54 52 253 .68 .617 80 2230 6290 117 125 91 99 0 749 164 585 .924 651 487 1.082 .992 -.114 -.011
5 16099 2325 192 210 15907 2115 762 873 2804 538 570 663 15 0 25306 3362 12011 1746 28 25 26 18 18022 1233 7.521 .133 1.163 .47 .743 4.315 120 614 .1 .741 130 2380 6260 111 124 103 116 -100 1860 168 1692 .106 698 530 9.401 .931 -3.233 -.104
6 604 732 194 225 410 507 604 708 198 228 410 483 0 0 127 184 48 51 100 100 100 100 917 893 .809 1.237 1.178 1.21 1.244 1.591 32 151 1.289 .712 60 2520 6290 118 124 121 127 0 586 180 406 .989 566 386 1.011 .942 -.016 -.085
7 532 641 185 220 347 421 529 640 189 223 344 420 0 0 110 147 42 63 100 100 100 100 768 764 .824 1.213 1.221 1.197 1.269 1.401 32 221 1.215 .762 70 2660 6280 116 123 134 141 0 513 176 337 .971 512 336 1.03 .977 -.043 -.034
8 770 868 189 220 581 648 737 863 217 247 548 643 0 0 319 334 160 169 90 96 78 84 1229 1191 .897 1.115 1.173 1.181 1.143 1.45 52 302 1.087 .884 90 2810 6290 116 125 148 157 0 694 176 518 .892 690 514 1.121 .939 -.164 -.091
9 765 1133 185 219 580 914 763 1127 207 239 578 908 0 0 111 178 132 144 100 100 100 100 1494 1486 .635 1.576 1.571 1.577 1.542 1.186 52 291 1.542 .886 90 2950 6280 115 124 162 171 0 906 175 731 1.261 902 726 .793 1.257 .334 .33
10 1339 1781 191 229 1148 1552 1415 1944 267 306 1224 1715 0 0 462 506 681 683 83 95 38 70 2700 2939 .74 1.352 1.401 1.48 1.326 1.603 80 345 1.163 .825 100 3100 6290 116 126 177 187 0 1425 183 1242 1.082 1555 1372 .925 1.121 .113 .165
11 769 884 185 225 584 659 784 888 189 225 599 663 0 0 136 117 42 54 100 100 100 100 1243 1262 .886 1.128 1.107 1.141 1.166 1.287 52 289 1.121 .846 90 3250 6280 115 124 192 201 0 707 180 527 .903 710 530 1.108 .886 -.148 -.175
12 1059 1413 190 227 869 1186 1086 1447 197 233 896 1220 0 0 234 235 50 62 100 100 100 100 2055 2116 .733 1.365 1.362 1.408 1.339 1.299 52 301 1.32 .914 90 3380 6280 115 124 205 214 0 1130 182 949 1.092 1158 976 .916 1.089 .127 .123
13 1278 1889 188 231 1090 1658 1279 1883 194 239 1091 1652 0 0 214 227 50 63 100 100 100 100 2748 2743 .657 1.521 1.514 1.537 1.477 1.164 52 312 1.471 .934 90 3530 6280 115 124 220 229 0 1511 185 1326 1.217 1506 1322 .822 1.211 .283 .277
14 1495 1925 194 237 1301 1688 1585 1998 208 255 1391 1761 0 0 329 377 93 123 100 100 100 100 2989 3152 .771 1.297 1.266 1.318 1.301 1.207 52 302 1.285 .947 90 3670 6280 115 124 234 243 0 1540 190 1350 1.038 1598 1409 .963 1.013 .054 .018
15 683 862 194 224 489 638 702 859 205 243 508 635 0 0 202 190 88 116 93 100 92 97 1127 1143 .766 1.305 1.25 1.421 1.33 1.643 80 336 1.264 .832 100 3820 6290 116 126 249 259 0 690 179 510 1.044 687 508 .958 1 .062 0
16 3536 5442 184 221 3352 5221 3588 5938 188 228 3404 5717 0 0 1304 1856 60 62 100 100 98 100 8573 9121 .642 1.558 1.679 1.628 1.554 1.346 80 366 1.54 .965 100 3970 6280 115 125 264 274 0 4354 177 4177 1.246 4751 4574 .802 1.344 .317 .426
17 1177 1568 184 230 993 1338 1146 1544 186 233 962 1314 0 0 226 260 47 57 100 100 100 100 2331 2276 .742 1.347 1.366 1.356 1.385 1.145 52 300 1.344 .93 90 4120 6280 115 124 279 288 0 1254 184 1070 1.078 1235 1051 .928 1.093 .108 .128
18 1624 1805 186 227 1438 1578 1606 1820 189 235 1420 1593 0 0 256 246 50 62 100 100 100 100 3016 3013 .911 1.097 1.122 1.101 1.11 1.144 52 300 1.081 .948 90 4270 6280 115 124 294 303 0 1444 182 1262 .878 1456 1274 1.139 .898 -.188 -.156
19 2600 3643 180 212 2420 3431 2681 3780 184 217 2501 3568 0 0 880 1170 45 59 100 100 98 100 5851 6069 .705 1.418 1.427 1.48 1.393 1.379 80 346 1.405 .957 100 4410 6280 115 125 308 318 0 2915 170 2745 1.134 3024 2855 .882 1.141 .182 .191
20 1028 1182 179 206 849 976 1054 1219 182 210 875 1013 0 0 222 266 41 50 100 100 100 100 1825 1888 .87 1.15 1.158 1.144 1.209 1.289 80 338 1.157 .92 100 4560 6280 115 125 323 333 0 946 165 781 .92 975 810 1.087 .926 -.121 -.111

Total number of rows: 41472

Table truncated, full table size 9608 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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