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Sample GSM148719 Query DataSets for GSM148719
Status Public on Oct 03, 2007
Title PT313_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47177.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT313_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT313_2 DNA
Prostate genomic DNA; LabeledExtract: 47177.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 = 880, 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 = 38.85; Parameter Scan Time = 10:59:33; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136066; 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 = 38.85; Parameter Scan Time = 10:59:33; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501132; 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/2003-12/47177.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
1 659 812 131 200 528 612 680 854 131 204 549 654 0 0 137 231 29 43 100 100 100 98 1140 1203 .863 1.159 1.191 1.084 1.147 1.486 52 286 1.215 .871 80 1670 6040 68 76 75 83 0 832 205 627 1.187 875 670 .842 1.22 .247 .287
2 824 835 132 209 692 626 897 900 132 213 765 691 0 0 260 232 31 46 100 100 100 98 1318 1456 1.105 .905 .903 .905 .85 1.505 52 267 .891 .868 80 1810 6050 69 77 89 97 0 855 214 641 .926 922 708 1.079 .925 -.11 -.112
3 1161 1135 128 198 1033 937 1223 1152 131 205 1095 954 0 0 244 233 28 45 100 100 100 100 1970 2049 1.102 .907 .871 .902 .915 1.259 52 258 .893 .912 80 1960 6050 69 77 104 112 0 1162 203 960 .929 1180 977 1.077 .892 -.106 -.165
4 865 719 130 199 735 520 865 730 131 204 735 531 0 0 111 117 29 52 100 100 100 100 1255 1266 1.413 .707 .722 .696 .695 1.254 32 210 .712 .832 70 2090 6040 68 75 117 124 0 736 204 533 .725 748 544 1.38 .74 -.465 -.435
5 1233 1137 131 202 1102 935 1187 1150 134 207 1056 948 0 0 242 209 33 49 100 100 100 100 2037 2004 1.179 .848 .898 .836 .878 1.359 52 334 .868 .896 90 2240 6040 67 76 131 140 0 1164 207 958 .869 1178 971 1.151 .919 -.203 -.121
6 720 778 129 189 591 589 773 797 132 196 644 608 0 0 167 127 34 46 100 100 100 100 1180 1252 1.003 .997 .944 1.034 .939 1.395 32 197 .927 .87 70 2370 6050 69 76 145 152 0 797 194 603 1.021 816 623 .98 .967 .029 -.049
7 970 984 124 191 846 793 960 1015 127 195 836 824 0 0 135 167 31 41 100 100 100 100 1639 1660 1.067 .937 .986 .921 .925 1.262 52 346 .963 .913 90 2530 6040 67 76 160 169 0 1008 196 812 .96 1039 844 1.042 1.009 -.059 .013
8 799 903 125 190 674 713 785 888 128 192 660 698 0 0 136 122 30 38 100 100 100 100 1387 1358 .945 1.058 1.058 1.069 1.025 1.29 52 290 1.046 .902 90 2680 6050 68 77 175 184 0 925 195 730 1.083 909 715 .923 1.083 .116 .115
9 544 611 125 184 419 427 549 612 128 189 424 428 0 0 101 120 29 40 100 100 100 100 846 852 .981 1.019 1.009 1.007 1.004 1.301 52 303 1.044 .845 90 2820 6040 67 76 189 198 0 626 188 437 1.044 627 438 .958 1.034 .062 .048
10 910 886 127 192 783 694 951 869 130 194 824 677 0 0 192 178 29 42 100 100 100 100 1477 1501 1.128 .886 .822 .886 .895 1.247 52 303 .888 .898 90 2970 6040 67 76 204 213 0 907 197 711 .908 890 693 1.102 .841 -.14 -.249
11 483 561 128 193 355 368 473 554 129 197 345 361 0 0 66 89 29 40 100 100 100 100 723 706 .965 1.037 1.046 1.023 1.026 1.331 52 315 1.05 .821 90 3120 6040 67 76 219 228 0 575 198 377 1.062 567 370 .942 1.072 .086 .1
12 615 699 123 189 492 510 627 700 125 191 504 511 0 0 104 112 29 43 100 100 100 100 1002 1015 .965 1.037 1.014 1.034 1.033 1.294 52 316 1.056 .848 90 3270 6040 67 76 234 243 0 716 194 522 1.062 717 523 .942 1.038 .086 .054
13 754 910 127 188 627 722 740 910 126 192 613 722 0 0 95 115 30 44 100 100 100 100 1349 1335 .868 1.152 1.178 1.149 1.15 1.183 52 288 1.177 .903 90 3410 6040 67 76 248 257 0 932 193 739 1.179 932 739 .848 1.206 .238 .27
14 792 898 130 188 662 710 858 954 131 190 728 766 0 0 258 252 29 42 100 100 98 98 1372 1494 .932 1.073 1.052 1.111 1.064 1.704 80 380 1.046 .874 100 3560 6040 67 77 263 273 0 920 193 727 1.098 977 784 .91 1.078 .135 .108
15 504 545 127 184 377 361 498 551 128 189 371 367 0 0 98 84 29 43 100 100 100 100 738 738 1.044 .958 .989 .966 .98 1.359 52 276 .972 .802 90 3710 6040 67 76 278 287 0 558 188 370 .981 564 376 1.02 1.013 -.028 .019
16 1771 2169 129 193 1642 1976 1763 2209 134 199 1634 2016 0 0 472 456 48 51 100 100 100 100 3618 3650 .831 1.203 1.234 1.22 1.206 1.195 52 335 1.185 .938 90 3850 6040 67 76 292 301 0 2221 198 2024 1.232 2262 2065 .811 1.264 .301 .337
17 1315 1046 130 188 1185 858 889 1041 131 194 759 853 0 0 1748 288 30 45 100 100 100 100 2043 1612 1.381 .724 1.124 .961 1.086 1.73 52 262 .235 .295 80 4010 6040 68 76 309 317 0 1071 193 879 .741 1066 874 1.349 1.151 -.431 .203
18 841 883 127 187 714 696 848 893 129 186 721 706 0 0 120 131 30 43 100 100 100 100 1410 1427 1.026 .975 .979 .969 .968 1.225 52 288 .997 .907 90 4150 6040 67 76 322 331 0 904 192 713 .998 915 723 1.002 1.003 -.002 .004
19 2357 2547 128 183 2229 2364 2192 2407 131 187 2064 2224 0 0 765 591 31 43 100 100 100 100 4593 4288 .943 1.061 1.078 1.081 1.087 1.205 52 288 1.031 .933 90 4290 6040 67 76 336 345 0 2608 187 2421 1.086 2465 2278 .921 1.103 .119 .142
20 638 576 127 176 511 400 657 590 128 180 530 414 0 0 208 168 30 43 100 100 100 97 911 944 1.278 .783 .781 .758 .811 1.455 80 396 .76 .845 100 4440 6040 67 77 351 361 0 590 180 410 .802 604 424 1.247 .8 -.319 -.322

Total number of rows: 41664

Table truncated, full table size 9566 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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