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Sample GSM91929 Query DataSets for GSM91929
Status Public on Jan 12, 2006
Title PPCvsXY
Sample type genomic
 
Channel 1
Source name XY genomic DNA
Organism Homo sapiens
Characteristics XY genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name PPC genomic DNA
Organism Homo sapiens
Characteristics PPC genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35082.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 Jan 11, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3355
Series (2)
GSE4017 DNA copy number changes in prostate cancer cell lines
GSE4396 Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 2933 942 335 233 2598 709 703 315 349 242 368 82 0 0 9777 2225 117 86 93 50 75 34 3307 450 3.664 .273 .223 .337 .347 2.592 32 171 .228 .98 60 2280 9050 78 84 47 53 -100 1108 274 834 .321 371 96 3.115 .262 -1.639 -1.932
2 909 643 325 256 584 387 886 621 359 285 561 365 0 0 270 175 225 166 93 87 71 62 971 926 1.509 .663 .651 .632 .712 2.144 32 214 .53 .71 70 2430 9050 77 84 61 68 0 756 301 455 .78 731 429 1.283 .765 -.359 -.386 -.386
3 719 346 329 239 390 107 456 295 357 262 127 56 0 0 534 170 165 124 43 40 31 25 497 183 3.645 .274 .441 .352 .35 2.227 32 172 .269 .54 60 2560 9050 78 84 75 81 0 407 281 126 .323 347 66 3.098 .519 -1.631 -.947 -.947
4 821 399 369 227 452 172 683 319 375 248 314 92 0 0 489 218 113 134 65 46 62 31 624 406 2.628 .381 .293 .383 .401 2.006 32 171 .396 .52 60 2700 9050 78 84 89 95 0 469 267 202 .448 375 108 2.234 .345 -1.159 -1.537 -1.537
5 1477 737 408 209 1069 528 1586 808 423 223 1178 599 0 0 329 229 115 83 100 100 100 91 1597 1777 2.025 .494 .508 .461 .508 1.313 12 104 .465 .89 50 2860 9040 77 82 105 110 0 867 246 621 .581 951 705 1.721 .598 -.783 -.741 -.741
6 1245 1103 402 275 843 828 1310 1137 677 328 908 862 0 0 369 277 2283 478 0 84 0 40 1671 1770 1.018 .982 .949 1.008 .864 1.564 32 220 .046 .18 70 3010 9040 76 83 119 126 0 1298 324 974 1.156 1338 1014 .865 1.117 .209 .159 .159
7 1235 663 388 285 847 378 1049 563 488 350 661 278 0 0 971 595 586 533 53 21 34 6 1225 939 2.241 .446 .421 .437 .438 1.724 32 176 .529 .88 60 3150 9050 78 84 134 140 0 780 335 445 .525 662 327 1.905 .495 -.93 -1.015 -1.015
8 1073 526 384 274 689 252 1021 496 405 312 637 222 0 0 281 195 184 201 96 62 90 12 941 859 2.734 .366 .349 .324 .401 2.302 32 204 .384 .53 70 3310 9050 77 84 149 156 0 619 322 296 .43 584 261 2.324 .41 -1.217 -1.286 -1.286
9 960 565 365 268 595 297 930 542 390 296 565 274 0 0 278 159 195 155 96 82 73 46 892 839 2.003 .499 .485 .489 .522 1.966 52 286 .521 .59 80 3440 9050 77 85 162 170 0 665 315 349 .587 638 322 1.703 .571 -.768 -.81 -.81
10 10659 2045 365 287 10294 1758 1075 619 725 325 710 332 0 0 18569 2889 3327 178 34 62 28 46 12052 1042 5.856 .171 .468 .397 .287 4.673 32 156 .142 .89 60 3600 9030 76 82 179 185 -100 2406 338 2068 .201 728 391 4.977 .55 -2.315 -.862
11 899 461 338 271 561 190 868 443 667 299 530 172 0 0 271 127 2797 159 0 51 0 13 751 702 2.953 .339 .325 .346 .345 2.151 52 288 .005 .07 80 3740 9050 77 85 192 200 0 542 319 224 .398 521 202 2.51 .382 -1.328 -1.389 -1.389
12 1163 1173 335 267 828 906 1064 740 490 282 729 473 0 0 584 1883 1516 103 9 100 0 96 1734 1202 .914 1.094 .649 .79 .671 1.843 32 218 3.498 .52 70 3890 9050 77 84 207 214 0 1380 314 1066 1.287 871 556 .777 .763 .364 -.39 -.39
13 1110 709 329 256 781 453 1116 684 344 277 787 428 0 0 706 205 114 120 96 98 92 84 1234 1215 1.724 .58 .544 .624 .677 1.989 52 254 .379 .67 80 4030 9050 77 85 221 229 0 834 301 533 .682 805 504 1.465 .64 -.551 -.644 -.644
14 1548 1242 343 257 1205 985 1550 1273 364 276 1207 1016 0 0 408 299 166 127 100 100 100 100 2190 2223 1.223 .817 .842 .82 .819 1.342 80 349 .782 .91 100 4170 9050 76 86 234 244 0 1461 302 1159 .962 1498 1195 1.04 .99 -.056 -.014 -.014
15 881 676 330 249 551 427 862 678 343 251 532 429 0 0 234 185 106 80 97 98 93 92 978 961 1.29 .775 .806 .774 .79 1.728 80 350 .743 .81 100 4320 9050 76 86 249 259 0 795 293 502 .912 798 505 1.097 .949 -.133 -.076 -.076
16 2102 1699 311 235 1791 1464 2131 1662 330 245 1820 1427 0 0 598 402 122 92 100 100 100 100 3255 3247 1.223 .817 .784 .837 .839 1.3 80 331 .784 .95 100 4470 9050 76 86 264 274 0 1999 276 1722 .962 1955 1679 1.04 .922 -.056 -.116 -.116
17 1582 1106 317 227 1265 879 1611 1115 328 238 1294 888 0 0 591 339 109 76 100 100 100 100 2144 2182 1.439 .695 .686 .722 .698 1.424 80 395 .667 .88 110 4610 9050 75 86 277 288 0 1301 267 1034 .817 1312 1045 1.223 .807 -.291 -.309 -.309
18 339 256 311 231 28 25 303 254 322 236 -8 23 0 0 135 85 101 72 17 21 5 15 53 15 1.12 .893 null .786 .615 3.608 52 244 -1 -1 80 4750 9040 76 84 293 301 -50 301 272 29 1.05 299 27 .952 null .071 null
19 1867 1841 302 231 1565 1610 1894 1957 312 241 1592 1726 0 0 699 628 89 83 98 100 95 100 3175 3318 .972 1.029 1.084 1.097 1.025 1.598 80 354 1.003 .95 100 4900 9050 76 86 307 317 0 2166 272 1894 1.21 2302 2031 .826 1.275 .275 .351 .351
20 1030 696 301 231 729 465 1002 683 321 250 701 452 0 0 333 210 161 181 95 92 88 65 1194 1153 1.568 .638 .645 .635 .625 1.739 80 324 .573 .85 100 5050 9050 76 86 322 332 0 819 272 547 .75 804 532 1.333 .759 -.414 -.399 -.399

Total number of rows: 43008

Table truncated, full table size 9923 Kbytes.




Supplementary data files not provided
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