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Sample GSM148732 Query DataSets for GSM148732
Status Public on Oct 03, 2007
Title PT100_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47182.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT100_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT100_1 DNA
Prostate genomic DNA; LabeledExtract: 47182.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 = 760, 4720; 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 = 38.44; Parameter Scan Time = 08:47:38; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136732; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; 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 = 38.44; Parameter Scan Time = 08:47:38; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501797; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.06; 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/2003-12/47182.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 1121 1149 182 285 939 864 1183 1178 183 291 1001 893 0 0 257 180 42 61 100 100 100 100 1803 1894 1.087 .92 .892 .957 .945 1.366 52 342 .879 .88 90 1580 5610 84 93 77 86 0 1262 313 949 1.011 1294 981 .99 .98 .015 -.029
2 1563 1252 192 303 1371 949 1597 1275 195 311 1405 972 0 0 239 282 47 69 100 100 100 100 2320 2377 1.445 .692 .692 .663 .696 1.282 32 214 .71 .902 70 1720 5600 84 91 92 99 0 1375 333 1042 .76 1400 1068 1.315 .76 -.395 -.396
3 2080 1386 192 289 1888 1097 2068 1411 195 292 1876 1122 0 0 578 473 46 63 100 98 100 96 2985 2998 1.721 .581 .598 .512 .593 1.686 52 330 .608 .926 90 1870 5600 83 92 106 115 0 1522 317 1205 .638 1550 1232 1.567 .657 -.648 -.606
4 589 162 188 287 401 -125 579 166 193 290 391 -121 0 0 86 42 48 52 100 0 100 0 276 270 null null null 0 0 1 32 201 2.616 .497 70 2000 5600 84 91 120 127 0 178 315 -137 null 182 -133 null null null null
5 2156 1863 181 276 1975 1587 2196 1967 185 281 2015 1691 0 0 551 591 45 58 100 100 100 100 3562 3706 1.244 .804 .839 .739 .834 1.719 80 405 .82 .894 100 2150 5600 83 93 134 144 0 2046 303 1743 .883 2160 1857 1.133 .922 -.18 -.118
6 1110 968 184 275 926 693 1106 960 187 277 922 685 0 0 172 259 44 60 100 100 100 100 1619 1607 1.336 .748 .743 .7 .73 1.43 32 207 .756 .839 70 2300 5600 84 91 150 157 0 1063 302 761 .822 1054 752 1.217 .816 -.283 -.293
7 1731 1657 177 270 1554 1387 1760 1749 181 273 1583 1479 0 0 312 544 40 56 100 98 100 94 2941 3062 1.12 .893 .934 .75 .913 2.036 52 314 .95 .908 90 2450 5600 83 92 164 173 0 1820 297 1523 .98 1921 1624 1.02 1.026 -.029 .037
8 1429 1428 177 266 1252 1162 1399 1397 180 267 1222 1131 0 0 265 217 40 56 100 100 100 100 2414 2353 1.077 .928 .926 .934 .943 1.21 52 286 .894 .882 90 2590 5610 84 93 178 187 0 1568 292 1276 1.019 1534 1242 .981 1.017 .028 .024
9 919 937 175 260 744 677 935 960 180 262 760 700 0 0 153 233 44 53 100 100 100 96 1421 1460 1.099 .91 .921 .833 .963 1.671 52 324 .929 .777 90 2740 5600 83 92 193 202 0 1029 286 744 .999 1054 769 1.001 1.012 -.001 .017
10 1377 1169 178 267 1199 902 1374 1180 179 268 1196 913 0 0 242 255 42 56 100 100 100 100 2101 2109 1.329 .752 .763 .733 .771 1.325 52 314 .771 .879 90 2890 5600 83 92 208 217 0 1284 293 991 .826 1296 1003 1.21 .838 -.275 -.254
11 813 841 172 258 641 583 798 888 177 259 626 630 0 0 123 186 40 54 100 100 100 98 1224 1256 1.099 .91 1.006 .857 .883 1.602 52 254 .945 .79 80 3040 5600 84 92 224 232 0 924 283 640 .999 975 692 1.001 1.105 -.002 .144
12 983 963 179 261 804 702 996 996 180 260 817 735 0 0 153 211 38 54 100 100 100 96 1506 1552 1.145 .873 .9 .817 .881 1.511 52 254 .899 .861 80 3180 5600 84 92 238 246 0 1058 287 771 .959 1094 807 1.043 .988 -.06 -.017
13 1278 1433 182 275 1096 1158 1314 1450 182 275 1132 1175 0 0 157 245 37 54 100 100 100 100 2254 2307 .946 1.057 1.038 1.041 1.072 1.24 52 264 1.074 .877 80 3330 5600 84 92 253 261 0 1574 302 1272 1.16 1593 1291 .862 1.14 .215 .189
14 1442 1430 182 260 1260 1170 1471 1577 186 263 1289 1317 0 0 202 452 43 57 100 96 100 90 2430 2606 1.077 .929 1.022 .845 .988 1.858 52 329 1.026 .879 90 3480 5590 82 91 267 276 0 1571 286 1285 1.02 1732 1446 .981 1.122 .028 .166
15 778 941 181 261 597 680 773 971 182 262 592 710 0 0 146 174 40 55 100 100 100 100 1277 1302 .878 1.139 1.199 1.127 1.167 1.35 52 288 1.145 .813 90 3630 5600 83 92 282 291 0 1034 287 747 1.251 1066 780 .799 1.317 .323 .398
16 2967 3393 177 257 2790 3136 3075 3330 178 259 2898 3073 0 0 568 751 40 54 100 100 100 100 5926 5971 .89 1.124 1.06 1.115 1.13 1.158 52 301 1.128 .938 90 3770 5600 83 92 296 305 0 3727 282 3444 1.235 3657 3375 .81 1.165 .304 .22
17 1312 1484 182 254 1130 1230 1231 1442 180 258 1049 1188 0 0 250 354 41 58 100 100 100 100 2360 2237 .919 1.088 1.133 1.064 1.09 1.353 52 242 1.113 .886 80 3920 5600 84 92 312 320 0 1630 279 1351 1.196 1584 1305 .836 1.244 .258 .315
18 1514 1311 176 260 1338 1051 1503 1360 189 266 1327 1100 0 0 272 284 198 55 100 100 100 100 2389 2427 1.273 .786 .829 .764 .794 1.316 52 263 .729 .802 80 4060 5600 84 92 326 334 0 1440 286 1154 .863 1494 1208 1.159 .91 -.213 -.135
19 3433 3122 175 248 3258 2874 3387 3251 177 251 3212 3003 0 0 671 1101 37 55 100 100 100 98 6132 6215 1.134 .882 .935 .743 .935 2.233 52 302 .942 .875 90 4220 5590 82 91 341 350 0 3429 272 3157 .969 3571 3298 1.032 1.027 -.046 .038
20 1294 557 172 246 1122 311 1262 562 179 247 1090 316 0 0 371 139 41 57 100 98 100 93 1433 1406 3.608 .277 .29 .262 .282 1.694 80 365 .272 .767 100 4360 5600 83 93 355 365 0 612 270 342 .304 617 347 3.285 .318 -1.716 -1.651

Total number of rows: 41664

Table truncated, full table size 9623 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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