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Sample GSM148758 Query DataSets for GSM148758
Status Public on Oct 03, 2007
Title PT174_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47165.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT174_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT174_2 DNA
Prostate genomic DNA; LabeledExtract: 47165.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, 5530; 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 = 38.46; Parameter Scan Time = 11:00:45; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135299; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.48; 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 = 38.46; Parameter Scan Time = 11:00:45; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500364; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; 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/2003-12/47165.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
1 672 552 155 201 517 351 657 571 155 206 502 370 0 0 142 184 34 54 100 94 100 86 868 872 1.473 .679 .737 .612 .666 1.739 52 286 .74 .688 80 1900 6210 64 72 74 82 0 686 250 436 .844 710 460 1.185 .916 -.244 -.126
2 1018 643 155 209 863 434 1105 684 158 213 950 475 0 0 283 214 38 57 100 92 100 88 1297 1425 1.988 .503 .5 .464 .5 1.639 52 312 .532 .811 90 2040 6210 63 72 87 96 0 800 260 540 .625 851 591 1.599 .622 -.677 -.686
3 1391 1052 158 208 1233 844 1389 1104 161 213 1231 896 0 0 191 219 38 55 100 100 100 100 2077 2127 1.461 .685 .728 .66 .692 1.327 52 324 .707 .897 90 2180 6210 63 72 101 110 0 1308 259 1049 .851 1373 1114 1.175 .905 -.233 -.144
4 1003 562 159 206 844 356 1018 580 163 213 859 374 0 0 146 138 34 58 100 100 100 96 1200 1233 2.371 .422 .435 .391 .437 1.528 32 204 .416 .692 70 2330 6210 64 71 117 124 0 699 256 443 .524 721 465 1.907 .541 -.931 -.885
5 1583 1174 168 217 1415 957 1577 1192 175 228 1409 975 0 0 323 237 59 70 100 100 100 100 2372 2384 1.479 .676 .692 .674 .672 1.21 52 320 .667 .907 90 2460 6210 63 72 129 138 0 1460 270 1190 .841 1482 1212 1.189 .86 -.25 -.217
6 813 579 175 239 638 340 818 558 181 243 643 319 0 0 95 161 63 65 100 96 100 90 978 962 1.876 .533 .496 .476 .479 1.797 32 212 .58 .634 70 2610 6210 64 71 145 152 0 720 297 423 .663 694 397 1.509 .617 -.594 -.697
7 1265 1095 167 221 1098 874 1272 1102 170 228 1105 881 0 0 192 155 37 55 100 100 100 100 1972 1986 1.256 .796 .797 .798 .796 1.235 52 313 .816 .892 90 2760 6210 63 72 159 168 0 1362 275 1087 .99 1370 1095 1.01 .991 -.015 -.012
8 1161 916 164 212 997 704 1144 928 166 217 980 716 0 0 143 161 34 58 100 100 100 100 1701 1696 1.416 .706 .731 .693 .718 1.263 52 290 .702 .877 90 2900 6210 63 72 173 182 0 1139 264 875 .878 1154 890 1.139 .908 -.188 -.138
9 864 499 160 202 704 297 889 495 162 206 729 293 0 0 272 122 37 57 100 97 98 93 1001 1022 2.37 .422 .402 .41 .405 1.759 80 364 .395 .703 100 3050 6210 63 73 188 198 0 620 251 369 .525 616 364 1.906 .5 -.931 -1.001
10 1175 902 162 202 1013 700 1272 948 165 202 1110 746 0 0 366 217 39 52 98 100 96 98 1713 1856 1.447 .691 .672 .765 .68 1.844 80 312 .656 .882 100 3210 6220 64 74 204 214 0 1122 251 870 .859 1179 928 1.164 .836 -.219 -.259
11 775 614 160 204 615 410 776 617 164 205 616 413 0 0 112 74 37 47 100 100 100 100 1025 1029 1.5 .667 .67 .668 .695 1.271 52 272 .659 .803 90 3340 6210 63 72 217 226 0 763 254 510 .829 767 514 1.206 .834 -.271 -.262
12 984 779 160 199 824 580 992 781 165 200 832 582 0 0 143 114 36 51 100 100 100 100 1404 1414 1.421 .704 .7 .701 .694 1.2 52 328 .719 .858 90 3490 6210 63 72 232 241 0 969 247 721 .875 971 724 1.143 .87 -.192 -.201
13 1086 962 155 184 931 778 1078 966 159 189 923 782 0 0 98 118 38 50 100 100 100 100 1709 1705 1.197 .836 .847 .831 .846 1.203 52 300 .846 .878 90 3640 6210 63 72 247 256 0 1196 229 967 1.039 1201 972 .962 1.053 .055 .075
14 1178 1056 152 179 1026 877 1262 1098 154 182 1110 919 0 0 266 244 35 50 100 98 100 98 1903 2029 1.17 .855 .828 .838 .844 1.518 80 351 .85 .894 100 3790 6210 63 73 262 272 0 1313 223 1090 1.063 1365 1143 .941 1.029 .088 .042
15 716 588 154 183 562 405 719 568 157 185 565 385 0 0 65 98 34 51 100 100 100 100 967 950 1.388 .721 .681 .704 .718 1.297 52 276 .745 .792 90 3930 6210 63 72 276 285 0 731 228 504 .896 706 479 1.116 .847 -.158 -.239
16 2864 2479 155 196 2709 2283 2919 2518 160 198 2764 2322 0 0 408 391 35 52 100 100 100 100 4992 5086 1.187 .843 .84 .84 .846 1.124 52 312 .858 .929 90 4080 6210 63 72 291 300 0 3082 244 2839 1.048 3131 2887 .954 1.045 .068 .063
17 1349 1203 155 191 1194 1012 1359 1213 159 195 1204 1022 0 0 230 178 34 53 100 100 100 100 2206 2226 1.18 .848 .849 .852 .844 1.238 52 276 .829 .904 90 4220 6210 63 72 305 314 0 1496 237 1258 1.054 1508 1271 .949 1.055 .076 .078
18 1148 1028 150 184 998 844 1258 1092 153 188 1108 908 0 0 330 288 35 48 100 100 100 100 1842 2016 1.182 .846 .819 .845 .838 1.35 80 353 .842 .907 100 4370 6210 63 73 320 330 0 1278 229 1049 1.052 1358 1129 .951 1.019 .073 .027
19 3109 2671 151 188 2958 2483 3183 2801 152 193 3032 2613 0 0 812 649 34 49 100 100 100 100 5441 5645 1.191 .839 .862 .855 .821 1.506 80 360 .83 .919 100 4530 6210 63 73 336 346 0 3321 234 3087 1.044 3483 3249 .958 1.072 .062 .1
20 1142 744 153 188 989 556 1208 763 156 194 1055 575 0 0 245 185 37 50 100 100 100 97 1545 1630 1.779 .562 .545 .54 .546 1.383 80 345 .558 .875 100 4680 6210 63 73 351 361 0 925 234 691 .699 949 715 1.431 .678 -.517 -.561

Total number of rows: 41664

Table truncated, full table size 9532 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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