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Sample GSM148713 Query DataSets for GSM148713
Status Public on Oct 03, 2007
Title PT14_3 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52827.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT14_3 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT14_3 DNA
Prostate genomic DNA; LabeledExtract: 52827.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 = 1480, 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 = 38.91; Parameter Scan Time = 10:45:59; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166611; 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 = 38.91; Parameter Scan Time = 10:45:59; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; 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/2004-06/52827.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
1 445 444 181 230 264 214 455 438 185 230 274 208 0 0 92 93 41 62 98 96 96 86 478 482 1.234 .811 .759 .803 .798 1.884 52 281 .941 .496 80 1950 6410 65 73 43 51 0 450 233 217 .822 444 211 1.216 .77 -.282 -.377
2 818 814 183 229 635 585 843 801 189 236 660 572 0 0 132 154 52 82 100 100 100 96 1220 1232 1.085 .921 .867 .896 .881 1.414 32 224 .93 .796 70 2090 6400 64 71 57 64 0 826 232 593 .935 813 580 1.07 .879 -.098 -.186
3 560 528 184 219 376 309 557 521 186 224 373 302 0 0 71 92 42 66 100 100 100 100 685 675 1.217 .822 .81 .801 .818 1.447 32 220 .852 .691 70 2240 6410 65 72 72 79 0 536 222 313 .834 529 306 1.199 .821 -.262 -.284
4 491 474 181 225 310 249 490 462 184 230 309 237 0 0 93 90 41 66 100 100 100 93 559 546 1.245 .803 .767 .788 .856 1.65 32 221 .815 .542 70 2380 6400 64 71 86 93 0 481 228 253 .815 469 240 1.227 .778 -.295 -.362
5 482 469 184 224 298 245 477 471 187 228 293 247 0 0 95 119 44 63 100 96 94 84 543 540 1.216 .822 .843 .828 .846 1.654 52 349 .91 .575 90 2530 6400 63 72 100 109 0 476 227 249 .834 478 251 1.199 .855 -.262 -.226
6 447 382 198 232 249 150 453 386 193 236 255 154 0 0 74 99 43 60 100 81 96 62 399 409 1.66 .602 .604 .543 .625 2.478 32 215 .727 .324 70 2680 6410 65 72 116 123 0 388 235 152 .611 392 156 1.636 .613 -.71 -.707
7 543 422 188 222 355 200 560 423 191 231 372 201 0 0 115 81 39 66 96 96 96 78 555 573 1.775 .563 .54 .537 .569 2.195 32 171 .531 .421 60 2820 6410 66 72 131 137 0 428 225 203 .572 429 204 1.75 .548 -.807 -.867
8 607 520 190 223 417 297 560 515 191 230 370 292 0 0 114 123 44 72 100 100 100 84 714 662 1.404 .712 .789 .668 .723 1.68 32 204 .739 .606 70 2970 6410 65 72 145 152 0 528 226 301 .723 522 296 1.384 .801 -.469 -.321
9 555 608 187 221 368 387 510 570 187 234 323 349 0 0 256 250 45 71 100 100 100 100 755 672 .951 1.052 1.08 1.043 1.039 1.535 52 304 1.036 .724 90 3110 6400 63 72 158 167 0 617 224 393 1.067 578 354 .937 1.096 .093 .132
10 608 692 182 219 426 473 641 685 185 226 459 466 0 0 156 149 43 64 97 100 96 100 899 925 .901 1.11 1.015 1.139 1.083 1.498 80 356 1.094 .789 100 3260 6400 63 73 173 183 0 702 222 480 1.126 695 473 .888 1.03 .172 .043
11 482 488 183 230 299 258 496 485 186 234 313 255 0 0 87 86 42 64 100 96 100 90 557 568 1.159 .863 .815 .835 .909 1.71 52 300 .899 .579 90 3410 6400 63 72 188 197 0 495 233 262 .875 492 259 1.142 .827 -.192 -.275
12 541 652 186 235 355 417 530 641 191 238 344 406 0 0 119 116 56 68 100 100 98 98 772 750 .851 1.175 1.18 1.198 1.082 1.527 52 254 1.153 .69 80 3550 6400 64 72 203 211 0 661 238 423 1.192 650 412 .839 1.197 .253 .26
13 547 671 185 234 362 437 547 679 189 235 362 445 0 0 80 133 55 66 100 100 100 100 799 807 .828 1.207 1.229 1.181 1.197 1.408 52 264 1.296 .749 80 3700 6400 64 72 218 226 0 681 237 443 1.225 689 451 .817 1.247 .292 .319
14 683 730 190 241 493 489 671 732 191 243 481 491 0 0 123 158 41 64 100 100 100 100 982 972 1.008 .992 1.021 .97 .985 1.455 52 300 1.051 .752 90 3840 6400 63 72 231 240 0 741 244 496 1.006 743 498 .994 1.036 .009 .05
15 476 485 185 246 291 239 472 462 188 250 287 216 0 0 93 121 44 71 100 92 100 82 530 503 1.218 .821 .753 .758 .833 1.867 52 300 1.007 .529 90 3990 6400 63 72 246 255 0 492 250 242 .833 469 219 1.2 .764 -.263 -.389
16 1520 2103 183 243 1337 1860 1512 2169 185 249 1329 1926 0 0 344 485 43 69 100 100 100 100 3197 3255 .719 1.391 1.449 1.388 1.406 1.226 52 312 1.403 .947 90 4130 6400 63 72 260 269 0 2133 247 1887 1.411 2200 1954 .709 1.47 .497 .556
17 906 1051 184 245 722 806 782 841 186 253 598 596 0 0 940 1173 38 71 100 100 100 100 1528 1194 .896 1.116 .997 1.055 1.135 1.464 52 252 1.21 .941 80 4280 6400 64 72 276 284 0 1066 249 818 1.133 853 605 .883 1.011 .18 .016
18 898 1030 183 238 715 792 898 1023 185 247 715 785 0 0 127 179 39 73 100 100 100 100 1507 1500 .903 1.108 1.098 1.097 1.128 1.282 52 242 1.133 .876 80 4430 6400 64 72 291 299 0 1045 241 803 1.124 1038 796 .89 1.114 .168 .156
19 1597 1914 183 247 1414 1667 1547 1878 188 253 1364 1631 0 0 321 335 41 77 100 100 100 100 3081 2995 .848 1.179 1.196 1.183 1.191 1.193 52 312 1.183 .935 90 4570 6400 63 72 304 313 0 1942 251 1691 1.196 1905 1655 .836 1.213 .258 .279
20 749 732 182 234 567 498 745 731 186 242 563 497 0 0 105 122 40 70 100 100 100 100 1065 1060 1.139 .878 .883 .866 .867 1.292 52 324 .911 .813 90 4720 6400 63 72 319 328 0 743 237 505 .891 742 504 1.122 .896 -.166 -.159

Total number of rows: 41472

Table truncated, full table size 9358 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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