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Sample GSM148728 Query DataSets for GSM148728
Status Public on Oct 03, 2007
Title PT126_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52834.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT126_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT126_1 DNA
Prostate genomic DNA; LabeledExtract: 52834.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, 5720; 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 = 39.49; Parameter Scan Time = 11:12:30; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 167954; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; 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 = 39.49; Parameter Scan Time = 11:12:30; Parameter PMT Volts = 750; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 532857; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.08; 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/2004-06/52834.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
1 946 965 175 208 771 757 977 954 177 217 802 746 0 0 185 206 40 77 100 100 100 100 1528 1548 1.018 .982 .93 .98 1.02 1.418 52 336 .995 .81 90 1830 6370 60 69 50 59 0 1002 216 786 1.019 990 774 .981 .966 .028 -.05
2 1316 1378 177 208 1139 1170 1339 1452 180 222 1162 1244 0 0 209 408 39 87 100 98 100 98 2309 2406 .974 1.027 1.071 .942 1.068 1.612 52 324 1.113 .846 90 1980 6370 60 69 65 74 0 1431 216 1215 1.066 1507 1291 .938 1.111 .093 .152
3 699 647 179 213 520 434 699 671 184 221 520 458 0 0 121 199 39 90 100 94 100 90 954 978 1.198 .835 .881 .784 .827 1.745 52 264 .92 .7 80 2130 6370 61 69 81 89 0 672 221 451 .866 697 475 1.154 .914 -.207 -.129
4 763 716 176 206 587 510 765 707 181 218 589 501 0 0 157 187 41 71 100 100 100 98 1097 1090 1.151 .869 .851 .833 .904 1.463 52 278 .92 .773 90 2270 6380 61 70 94 103 0 743 214 529 .902 734 520 1.109 .883 -.149 -.179
5 691 615 185 209 506 406 679 610 187 222 494 401 0 0 124 156 44 76 100 100 100 94 912 895 1.246 .802 .812 .758 .786 1.555 52 301 .84 .671 90 2410 6370 60 69 108 117 0 638 217 421 .833 633 416 1.201 .843 -.264 -.247
6 686 715 184 212 502 503 690 681 187 221 506 469 0 0 198 281 43 75 98 94 94 90 1005 975 .998 1.002 .927 1.069 1.017 1.876 52 264 1.125 .775 80 2560 6370 61 69 124 132 0 742 220 522 1.04 707 487 .961 .962 .057 -.056
7 616 524 180 218 436 306 628 525 186 225 448 307 0 0 95 166 42 79 100 92 100 78 742 755 1.425 .702 .685 .6 .678 2.027 52 264 .811 .616 80 2710 6370 61 69 139 147 0 544 226 318 .729 545 319 1.372 .711 -.457 -.491
8 749 736 181 214 568 522 737 732 185 220 556 518 0 0 185 210 38 78 100 100 100 96 1090 1074 1.088 .919 .932 .893 .95 1.553 52 262 .975 .728 90 2860 6380 61 70 153 162 0 764 222 542 .954 760 538 1.048 .967 -.068 -.048
9 691 719 182 224 509 495 691 719 185 225 509 495 0 0 115 185 39 76 100 100 100 98 1004 1004 1.028 .972 .972 .927 .924 1.535 80 365 1.046 .714 110 2990 6370 59 70 165 176 0 746 233 514 1.01 746 514 .991 1.01 .014 .014
10 1542 1542 187 226 1355 1316 1559 1533 189 228 1372 1307 0 0 246 332 41 73 100 100 100 100 2671 2679 1.03 .971 .953 .956 .968 1.245 80 370 .979 .897 110 3140 6370 59 70 180 191 0 1601 235 1366 1.008 1591 1357 .992 .989 .012 -.016
11 549 484 180 206 369 278 534 478 183 214 354 272 0 0 101 131 40 79 100 92 100 81 647 626 1.327 .753 .768 .677 .749 1.979 80 327 .801 .495 100 3290 6370 60 70 196 206 0 502 214 289 .782 496 282 1.279 .798 -.355 -.326
12 820 868 176 200 644 668 821 878 180 206 645 678 0 0 159 211 39 79 100 100 100 100 1312 1323 .964 1.037 1.051 1.015 1.03 1.449 80 376 1.062 .774 110 3430 6370 59 70 209 220 0 901 208 693 1.077 911 704 .929 1.091 .107 .126
13 1124 1196 180 199 944 997 1105 1158 182 206 925 959 0 0 177 247 39 74 100 100 100 100 1941 1884 .947 1.056 1.037 1.043 1.05 1.296 80 306 1.083 .816 100 3580 6370 60 70 225 235 0 1242 207 1035 1.096 1202 996 .912 1.076 .133 .106
14 1176 1258 179 207 997 1051 1265 1302 184 212 1086 1095 0 0 349 429 38 77 100 97 99 95 2048 2181 .949 1.054 1.008 1.004 1.055 1.685 120 416 1.11 .875 120 3720 6370 59 71 238 250 0 1306 215 1091 1.094 1352 1137 .914 1.047 .13 .066
15 627 642 177 209 450 433 617 629 180 219 440 420 0 0 93 136 40 82 100 100 100 100 883 860 1.039 .962 .955 .933 .927 1.47 80 357 1.006 .709 110 3870 6370 59 70 253 264 0 666 217 450 .999 653 436 1.001 .991 -.002 -.013
16 4753 4761 181 211 4572 4550 4739 4811 183 219 4558 4600 0 0 567 822 43 81 100 100 100 100 9122 9158 1.005 .995 1.009 .985 .985 1.185 80 376 .994 .933 110 4020 6370 59 70 268 279 0 4943 219 4724 1.033 4995 4775 .968 1.048 .047 .067
17 1335 1263 175 200 1160 1063 1358 1251 180 206 1183 1051 0 0 217 279 41 77 100 100 100 100 2223 2234 1.091 .916 .888 .896 .957 1.299 80 358 .934 .874 110 4170 6370 59 70 283 294 0 1311 208 1104 .951 1299 1091 1.051 .922 -.072 -.117
18 2167 2228 180 206 1987 2022 2175 2258 185 215 1995 2052 0 0 249 361 44 76 100 100 100 100 4009 4047 .983 1.018 1.029 1.009 1.016 1.186 80 338 1.026 .916 110 4310 6370 59 70 297 308 0 2313 214 2099 1.056 2344 2130 .947 1.068 .079 .095
19 3542 3553 181 205 3361 3348 3682 3529 186 215 3501 3324 0 0 651 729 45 77 100 100 100 100 6709 6825 1.004 .996 .949 .993 .989 1.213 80 364 .985 .926 110 4450 6370 59 70 311 322 0 3689 213 3476 1.034 3664 3451 .967 .986 .048 -.021
20 1231 1138 174 187 1057 951 1202 1129 177 198 1028 942 0 0 190 241 38 74 100 100 100 100 2008 1970 1.111 .9 .916 .885 .888 1.324 80 392 .904 .867 110 4600 6370 59 70 326 337 0 1181 194 987 .934 1172 978 1.071 .951 -.098 -.072

Total number of rows: 41472

Table truncated, full table size 9584 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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