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Sample GSM148739 Query DataSets for GSM148739
Status Public on Oct 03, 2007
Title PT83_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48743.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT83_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT83_2 DNA
Prostate genomic DNA; LabeledExtract: 48743.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 = 1080, 5200; 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 = 38.96; Parameter Scan Time = 11:27:10; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147902; 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 = 38.96; Parameter Scan Time = 11:27:10; Parameter PMT Volts = 670; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512805; 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/2004-01/48743.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
1 475 422 143 128 332 294 481 422 147 131 338 294 0 0 81 125 34 38 100 100 100 93 626 632 1.129 .886 .87 .8 .868 1.672 32 232 .906 .682 70 1860 6240 100 107 74 81 0 430 130 300 .903 430 300 1.108 .887 -.148 -.174
2 769 538 141 128 628 410 788 532 144 136 647 404 0 0 229 210 30 40 100 100 96 96 1038 1051 1.532 .653 .624 .628 .639 1.974 32 176 .66 .741 60 2000 6240 101 107 89 95 0 548 130 418 .666 542 412 1.503 .637 -.587 -.652
3 887 975 147 132 740 843 907 1013 151 142 760 881 0 0 181 303 41 57 100 100 100 100 1583 1641 .878 1.139 1.159 1.093 1.106 1.345 32 236 1.18 .882 70 2150 6240 100 107 103 110 0 994 135 859 1.161 1033 898 .861 1.182 .216 .241
4 660 422 150 132 510 290 672 444 148 133 522 312 0 0 139 152 34 42 100 90 100 87 800 834 1.759 .569 .598 .459 .584 2.331 32 164 .589 .76 60 2300 6240 101 107 119 125 0 430 135 296 .58 453 318 1.725 .609 -.787 -.715
5 831 743 144 136 687 607 858 773 145 140 714 637 0 0 222 253 35 38 100 100 100 100 1294 1351 1.132 .884 .892 .838 .87 1.402 52 288 .919 .885 80 2430 6250 101 109 131 139 0 757 139 619 .901 788 649 1.11 .909 -.151 -.137
6 636 187 144 132 492 55 645 187 151 133 501 55 0 0 108 67 41 39 100 56 100 28 547 556 8.945 .112 .11 .105 .131 2.758 32 168 .093 .133 60 2590 6240 101 107 148 154 0 191 135 56 .114 191 56 8.776 .112 -3.133 -3.16
7 717 630 139 124 578 506 749 625 143 128 610 501 0 0 188 203 33 40 98 100 98 98 1084 1111 1.142 .875 .821 .862 .871 1.62 52 274 .895 .859 80 2730 6250 101 109 161 169 0 642 126 516 .892 637 511 1.121 .837 -.164 -.256
8 692 766 144 132 548 634 696 754 147 139 552 622 0 0 165 246 37 45 100 100 100 100 1182 1174 .864 1.157 1.127 1.13 1.158 1.443 32 204 1.186 .866 70 2860 6240 100 107 174 181 0 781 135 646 1.179 769 634 .848 1.149 .238 .2
9 518 602 146 131 372 471 503 613 150 137 357 482 0 0 150 225 37 42 100 100 98 98 843 839 .79 1.266 1.35 1.216 1.178 1.558 52 276 .483 .338 80 3030 6250 101 109 191 199 0 614 134 480 1.291 625 491 .775 1.376 .368 .461
10 776 802 145 143 631 659 773 797 148 145 628 654 0 0 173 242 34 44 100 100 100 100 1290 1282 .958 1.044 1.041 1.016 1.036 1.356 52 247 1.099 .847 80 3170 6250 101 109 205 213 0 818 146 672 1.065 812 667 .939 1.062 .09 .086
11 572 504 142 146 430 358 576 512 145 149 434 366 0 0 117 157 31 46 100 100 100 96 788 800 1.201 .833 .843 .765 .842 1.578 32 171 .905 .806 60 3310 6240 101 107 220 226 0 514 149 365 .849 522 373 1.178 .86 -.237 -.218
12 601 595 146 134 455 461 587 557 149 141 441 423 0 0 144 198 35 53 100 100 100 100 916 864 .987 1.013 .959 .964 1.032 1.408 32 231 1.066 .806 70 3460 6240 100 107 234 241 0 607 137 470 1.033 568 431 .968 .978 .047 -.032
13 608 708 148 139 460 569 623 709 150 146 475 570 0 0 142 202 38 51 100 100 100 100 1029 1045 .808 1.237 1.2 1.242 1.216 1.463 52 261 1.272 .831 80 3610 6250 101 109 249 257 0 722 142 580 1.261 723 581 .793 1.223 .334 .291
14 696 773 147 139 549 634 705 759 149 141 558 620 0 0 208 288 33 39 100 98 98 98 1183 1178 .866 1.155 1.111 1.153 1.148 1.486 52 269 1.207 .891 80 3750 6240 100 108 263 271 0 788 142 646 1.177 774 632 .849 1.133 .235 .18
15 500 461 146 138 354 323 498 463 148 141 352 325 0 0 132 130 34 41 100 100 96 96 677 677 1.096 .912 .923 .897 .945 1.51 32 206 .938 .831 70 3890 6240 100 107 277 284 0 470 141 329 .93 472 331 1.075 .941 -.105 -.087
16 965 1183 145 144 820 1039 902 1151 150 148 757 1007 0 0 472 657 37 43 96 100 94 98 1859 1764 .789 1.267 1.33 1.281 1.284 2 52 306 1.324 .917 80 4040 6240 100 108 292 300 0 1206 147 1059 1.292 1173 1026 .774 1.356 .369 .439
17 554 597 142 140 412 457 569 596 149 147 427 456 0 0 203 201 46 45 96 100 93 100 869 883 .902 1.109 1.068 1.106 1.116 1.511 32 212 .998 .805 70 4190 6260 102 109 307 314 0 609 143 466 1.131 608 465 .884 1.089 .177 .122
18 729 767 139 132 590 635 716 786 143 136 577 654 0 0 225 296 33 41 100 100 100 94 1225 1231 .929 1.076 1.133 .972 1.116 1.661 52 286 1.124 .881 80 4350 6240 100 108 323 331 0 782 135 647 1.097 801 667 .911 1.155 .134 .208
19 1663 1892 143 139 1520 1753 1709 1939 148 144 1566 1800 0 0 530 663 38 42 100 100 100 100 3273 3366 .867 1.153 1.149 1.163 1.131 1.427 52 316 1.156 .928 90 4490 6240 99 108 336 345 0 1929 142 1787 1.176 1977 1835 .851 1.172 .233 .229
20 725 694 147 140 578 554 738 694 149 144 591 554 0 0 155 189 31 41 100 100 100 100 1132 1145 1.043 .958 .937 .931 .938 1.343 52 266 .978 .873 80 4640 6250 101 109 352 360 0 707 143 565 .977 707 565 1.024 .956 -.034 -.066

Total number of rows: 41664

Table truncated, full table size 9338 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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