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Sample GSM148727 Query DataSets for GSM148727
Status Public on Oct 03, 2007
Title PT195_3 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52833.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT195_3 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT195_3 DNA
Prostate genomic DNA; LabeledExtract: 52833.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, 5960; 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 = 38.92; Parameter Scan Time = 12:18:38; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167505; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; 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 = 38.92; Parameter Scan Time = 12:18:38; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532408; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; 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/2004-06/52833.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
1 434 436 136 112 298 324 454 420 140 116 318 308 0 0 111 140 35 34 100 100 98 96 622 626 .92 1.087 .969 1.071 1.073 1.609 52 278 1.14 .789 80 1990 6590 59 67 67 75 0 394 101 293 .984 380 279 1.017 .876 -.024 -.191
2 1161 1072 138 118 1023 954 1209 1091 144 121 1071 973 0 0 368 291 35 32 100 100 100 100 1977 2044 1.072 .933 .908 .99 .939 1.482 52 301 .899 .919 90 2130 6600 59 68 80 89 0 970 107 863 .844 987 880 1.185 .822 -.245 -.283
3 544 533 143 124 401 409 473 549 144 128 330 425 0 0 233 198 32 44 100 98 98 96 810 755 .98 1.02 1.288 1.07 .996 1.89 52 264 .984 .815 80 2280 6590 59 67 96 104 0 482 112 370 .923 497 384 1.084 1.165 -.116 .22
4 477 564 142 119 335 445 486 596 149 127 344 477 0 0 118 160 54 50 98 100 94 94 780 821 .753 1.328 1.387 1.313 1.244 1.647 52 274 1.085 .512 80 2430 6590 59 67 111 119 0 510 108 403 1.202 539 432 .832 1.254 .265 .327
5 531 634 144 125 387 509 508 607 153 129 364 482 0 0 267 360 70 36 100 100 94 98 896 846 .76 1.315 1.324 1.263 1.305 1.558 52 318 1.292 .787 90 2580 6590 58 67 125 134 0 574 113 460 1.19 549 436 .84 1.198 .251 .261
6 422 488 143 129 279 359 439 490 144 132 296 361 0 0 113 127 30 42 96 100 93 96 638 657 .777 1.287 1.22 1.251 1.319 1.575 32 204 1.201 .706 70 2710 6590 59 66 139 146 0 441 117 325 1.164 443 327 .859 1.103 .219 .142
7 479 477 151 120 328 357 456 507 153 124 305 387 0 0 150 135 49 38 100 96 96 93 685 692 .919 1.088 1.269 1.032 1.308 2.347 32 230 1.243 .504 70 2860 6580 58 65 154 161 0 432 109 323 .985 459 350 1.016 1.148 -.022 .199
8 685 791 152 131 533 660 660 802 163 137 508 671 0 0 125 184 88 54 100 100 100 100 1193 1179 .808 1.238 1.321 1.204 1.24 1.372 32 212 1.388 .757 70 3010 6580 58 65 169 176 0 716 119 597 1.12 726 607 .893 1.195 .164 .257
9 708 905 149 123 559 782 699 910 157 129 550 787 0 0 130 208 75 47 100 100 100 100 1341 1337 .715 1.399 1.431 1.374 1.439 1.382 52 305 1.5 .844 90 3150 6580 57 66 182 191 0 819 111 707 1.266 823 712 .79 1.295 .34 .372
10 948 1241 146 123 802 1118 961 1311 152 126 815 1188 0 0 450 545 44 41 100 100 98 100 1920 2003 .717 1.394 1.458 1.442 1.403 1.5 80 336 1.368 .875 100 3300 6590 58 68 197 207 0 1123 111 1011 1.261 1186 1075 .793 1.319 .335 .399
11 570 605 151 129 419 476 590 603 157 135 439 474 0 0 118 90 44 61 100 100 98 100 895 913 .88 1.136 1.08 1.19 1.157 1.52 52 288 1.075 .806 90 3440 6590 58 67 211 220 0 547 117 431 1.028 546 429 .973 .977 .04 -.034
12 700 758 149 118 551 640 679 762 154 125 530 644 0 0 145 133 41 59 100 100 100 100 1191 1174 .861 1.162 1.215 1.174 1.187 1.329 52 324 1.176 .843 90 3590 6580 57 66 226 235 0 686 107 579 1.051 689 583 .952 1.099 .072 .137
13 867 1135 154 119 713 1016 872 1136 159 123 718 1017 0 0 138 149 44 42 100 100 100 100 1729 1735 .702 1.425 1.416 1.437 1.399 1.234 52 312 1.449 .874 90 3740 6580 57 66 241 250 0 1027 108 919 1.289 1028 920 .776 1.281 .366 .358
14 1068 1305 155 128 913 1177 1061 1291 160 134 906 1163 0 0 194 166 39 42 100 100 100 100 2090 2069 .776 1.289 1.284 1.306 1.294 1.202 52 313 1.284 .911 90 3880 6580 57 66 255 264 0 1181 116 1065 1.166 1168 1052 .857 1.161 .222 .216
15 574 653 154 123 420 530 581 650 162 144 427 527 0 0 144 142 68 170 100 100 96 92 950 954 .792 1.262 1.234 1.302 1.256 1.466 80 347 1.241 .794 100 4030 6590 58 68 270 280 0 591 111 479 1.142 588 477 .876 1.117 .191 .159
16 2462 3432 157 124 2305 3308 2376 3576 174 167 2219 3452 0 0 938 1324 102 248 100 100 100 98 5613 5671 .697 1.435 1.556 1.401 1.488 1.353 52 305 1.53 .872 90 4170 6570 56 65 284 293 0 3105 112 2993 1.298 3235 3123 .77 1.407 .377 .493
17 854 1050 153 130 701 920 812 1038 182 161 659 908 0 0 199 193 268 250 100 100 80 100 1621 1567 .762 1.312 1.378 1.334 1.356 1.228 52 288 1.446 .848 90 4320 6580 57 66 299 308 0 950 118 832 1.187 939 821 .842 1.247 .248 .318
18 1122 1564 153 124 969 1440 1167 1631 178 153 1014 1507 0 0 254 292 261 244 98 100 92 100 2409 2521 .673 1.486 1.486 1.525 1.53 1.273 52 301 1.315 .659 90 4460 6580 57 66 313 322 0 1415 112 1303 1.344 1476 1363 .744 1.345 .427 .427
19 1887 2450 154 127 1733 2323 1841 2628 178 178 1687 2501 0 0 525 763 120 283 100 98 100 96 4056 4188 .746 1.34 1.483 1.294 1.361 1.404 52 305 1.421 .901 90 4610 6570 56 65 328 337 0 2216 115 2102 1.213 2378 2263 .825 1.341 .278 .424
20 710 718 157 127 553 591 760 790 170 146 603 663 0 0 246 237 101 141 91 96 90 83 1144 1266 .936 1.069 1.1 1.162 1.064 1.923 80 359 1.051 .86 100 4760 6580 57 67 343 353 0 650 115 535 .967 715 600 1.034 .995 -.049 -.008

Total number of rows: 41472

Table truncated, full table size 9389 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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