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Sample GSM148755 Query DataSets for GSM148755
Status Public on Oct 03, 2007
Title PT171_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47160.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT171_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT171_2 DNA
Prostate genomic DNA; LabeledExtract: 47160.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, 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 = 39.28; Parameter Scan Time = 12:46:30; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134337; 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 = 39.28; Parameter Scan Time = 12:46:30; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499402; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.24; 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/2003-11/47160.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
1 760 660 163 222 597 438 763 675 164 226 600 453 0 0 129 152 36 47 100 100 100 96 1035 1053 1.363 .734 .755 .686 .772 1.478 52 344 .755 .848 90 1810 6080 95 104 88 97 0 660 222 438 .733 675 453 1.363 .755 -.447 -.406
2 1111 627 159 234 952 393 1184 643 165 235 1025 409 0 0 279 210 39 49 100 96 100 92 1345 1434 2.422 .413 .399 .393 .43 1.58 52 267 .432 .771 80 1950 6080 96 104 103 111 0 627 234 393 .413 643 409 2.423 .399 -1.277 -1.326
3 1279 1133 166 231 1113 902 1317 1187 166 233 1151 956 0 0 230 227 36 53 100 100 100 100 2015 2107 1.234 .81 .831 .797 .812 1.271 52 306 .816 .92 90 2100 6090 96 105 117 126 0 1133 231 902 .81 1187 956 1.234 .83 -.304 -.268
4 1160 561 165 238 995 323 1189 564 168 238 1024 326 0 0 185 64 38 48 100 100 100 100 1318 1350 3.08 .325 .318 .324 .328 1.274 32 200 .31 .835 70 2230 6080 96 103 131 138 0 561 238 323 .325 564 326 3.082 .318 -1.624 -1.652
5 1201 912 161 223 1040 689 1261 948 167 225 1100 725 0 0 359 278 39 46 98 98 97 97 1729 1825 1.509 .663 .659 .623 .67 1.768 80 377 .663 .892 100 2380 6090 96 106 145 155 0 912 223 689 .662 948 725 1.51 .659 -.594 -.602
6 979 565 165 227 814 338 1009 569 168 227 844 342 0 0 141 96 36 46 100 100 100 100 1152 1186 2.408 .415 .405 .404 .394 1.26 32 212 .392 .813 70 2520 6080 96 103 160 167 0 565 227 338 .415 569 342 2.409 .405 -1.268 -1.304
7 1004 974 162 230 842 744 1022 995 167 234 860 765 0 0 174 162 39 46 100 100 100 100 1586 1625 1.132 .884 .89 .885 .87 1.23 52 332 .887 .909 90 2680 6080 95 104 175 184 0 974 230 744 .883 995 765 1.132 .889 -.179 -.169
8 897 315 162 227 735 88 899 295 168 231 737 68 0 0 151 105 41 47 100 67 100 36 823 805 8.352 .12 .092 .109 .103 2.26 52 302 .121 .246 90 2820 6080 95 104 189 198 0 315 227 88 .12 295 68 8.355 .092 -3.063 -3.439
9 654 626 167 233 487 393 650 637 169 235 483 404 0 0 95 134 38 46 100 100 100 100 880 887 1.239 .807 .836 .768 .844 1.417 52 274 .84 .796 80 2970 6080 96 104 205 213 0 626 233 393 .807 637 404 1.24 .836 -.31 -.258
10 1079 874 167 236 912 638 1089 900 171 237 922 664 0 0 195 148 41 49 100 100 100 100 1550 1586 1.429 .7 .72 .695 .698 1.225 52 302 .665 .879 90 3120 6080 95 104 219 228 0 874 236 638 .699 900 664 1.43 .72 -.516 -.474
11 594 549 173 229 421 320 601 531 176 229 428 302 0 0 89 100 41 48 100 100 100 100 741 730 1.316 .76 .706 .74 .76 1.419 52 254 .788 .783 80 3260 6080 96 104 234 242 0 549 229 320 .76 531 302 1.316 .705 -.396 -.504
12 798 647 180 235 618 412 802 651 181 237 622 416 0 0 138 103 40 47 100 100 100 100 1030 1038 1.5 .667 .669 .662 .679 1.348 52 274 .648 .845 80 3410 6080 96 104 249 257 0 647 235 412 .666 651 416 1.501 .669 -.585 -.581
13 800 902 178 234 622 668 804 908 181 239 626 674 0 0 130 124 37 43 100 100 100 100 1290 1300 .931 1.074 1.077 1.08 1.037 1.213 52 301 1.048 .898 90 3550 6080 95 104 262 271 0 902 234 668 1.074 908 674 .931 1.076 .102 .106
14 882 874 166 227 716 647 920 915 169 234 754 688 0 0 229 257 40 46 100 100 98 100 1363 1442 1.107 .904 .912 .873 .907 1.513 80 383 .924 .877 100 3710 6080 95 105 278 288 0 874 227 647 .903 915 688 1.107 .912 -.147 -.133
15 519 541 173 237 346 304 514 514 173 238 341 277 0 0 92 107 38 49 100 100 100 100 650 618 1.138 .879 .812 .855 .845 1.483 52 220 .837 .694 80 3850 6080 96 104 293 301 0 541 237 304 .878 514 277 1.139 .812 -.187 -.3
16 1680 1921 174 240 1506 1681 1576 1852 177 239 1402 1612 0 0 701 718 37 46 100 100 100 100 3187 3014 .896 1.116 1.15 1.141 1.115 1.261 52 311 1.095 .963 90 3990 6080 95 104 306 315 0 1920 240 1680 1.116 1851 1611 .896 1.149 .158 .201
17 940 962 174 234 766 728 902 983 177 238 728 749 0 0 221 242 38 49 100 100 100 100 1494 1477 1.052 .95 1.029 .932 .963 1.314 52 262 .957 .892 80 4150 6080 96 104 323 331 0 962 234 728 .95 983 749 1.053 1.028 -.074 .041
18 854 842 174 243 680 599 876 849 177 246 702 606 0 0 198 209 37 52 100 100 100 100 1279 1308 1.135 .881 .863 .851 .867 1.333 52 242 .893 .905 80 4290 6070 95 103 337 345 0 842 243 599 .881 849 606 1.136 .863 -.183 -.213
19 1920 1835 173 236 1747 1599 1649 1599 176 242 1476 1363 0 0 1045 919 50 60 100 100 97 98 3346 2839 1.093 .915 .923 .946 .932 1.401 80 377 .896 .95 100 4430 6070 94 104 350 360 0 1834 236 1598 .915 1598 1363 1.093 .923 -.128 -.115
20 759 514 168 238 591 276 762 504 175 243 594 266 0 0 138 100 53 55 100 100 100 96 867 860 2.141 .467 .448 .448 .459 1.438 52 324 .445 .778 90 4580 6070 94 103 365 374 0 514 238 276 .467 504 266 2.142 .448 -1.099 -1.16

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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