NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91931 Query DataSets for GSM91931
Status Public on Jan 12, 2006
Title LAPC4vsXY
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 LAPC4 genomic DNA
Organism Homo sapiens
Characteristics LAPC4 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35084.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 1209 757 326 223 883 534 954 746 354 235 628 523 0 0 1281 329 127 88 84 93 84 93 1417 1151 1.654 .605 .833 .929 .82 2.415 32 171 .292 .72 60 2270 9400 49 55 36 42 0 797 235 562 .637 785 551 1.571 .877 -.652 -.19 -.19
2 1160 1021 339 237 821 784 1132 968 379 236 793 731 0 0 365 295 331 75 90 100 68 100 1605 1524 1.047 .955 .922 1.021 .967 1.727 32 214 .556 .59 70 2410 9390 47 54 49 56 0 1075 249 825 1.005 1019 769 .995 .97 .007 -.043 -.043
3 1564 344 335 215 1229 129 410 276 351 230 75 61 0 0 5991 210 104 74 42 46 28 30 1358 136 9.527 .105 .813 .634 .594 4.057 52 278 .023 .53 80 2550 9390 47 55 63 71 -50 362 226 136 .11 291 64 9.051 .856 -3.178 -.224
4 849 558 338 232 511 326 601 428 432 261 263 196 0 0 490 294 652 273 37 46 9 25 837 459 1.567 .638 .745 .79 .684 2.226 32 224 .03 .22 70 2700 9390 47 54 78 85 0 587 244 343 .672 451 206 1.489 .784 -.574 -.35 -.35
5 1526 1105 336 251 1190 854 1777 1241 341 257 1441 990 0 0 574 407 100 79 100 100 100 100 2044 2431 1.393 .718 .687 .724 .739 1.305 12 104 .628 .89 50 2840 9390 48 53 93 98 0 1163 264 899 .755 1306 1042 1.324 .723 -.405 -.468 -.468
6 1288 1121 322 228 966 893 1340 1168 346 239 1018 940 0 0 503 325 193 100 96 100 84 100 1859 1958 1.082 .924 .923 1.016 .934 1.635 32 170 .831 .89 60 2990 9400 49 55 108 114 0 1180 240 940 .973 1229 989 1.028 .972 -.039 -.041 -.041
7 1140 683 341 231 799 452 1046 708 355 254 705 477 0 0 533 206 98 135 93 96 90 75 1251 1182 1.768 .566 .677 .69 .612 1.949 32 170 .447 .82 60 3140 9390 48 54 123 129 0 719 243 476 .595 745 502 1.679 .712 -.748 -.49 -.49
8 1172 1053 330 259 842 794 1186 1128 558 353 856 869 0 0 425 304 2308 912 0 40 0 0 1636 1725 1.06 .943 1.015 1.023 .879 2.047 32 226 .343 .8 70 3280 9390 47 54 136 143 0 1108 273 836 .993 1187 915 1.007 1.069 -.011 .096 .096
9 1049 766 312 242 737 524 1025 761 322 245 713 519 0 0 279 186 92 78 100 100 100 98 1261 1232 1.406 .711 .728 .715 .65 1.465 52 370 .647 .82 90 3440 9390 46 55 151 160 0 806 255 552 .748 801 546 1.336 .766 -.418 -.384 -.384
10 939 590 328 242 611 348 1003 543 331 242 675 301 0 0 257 144 83 72 100 100 100 100 959 976 1.756 .57 .446 .585 .555 1.66 12 104 .533 .85 50 3580 9400 49 54 167 172 0 621 255 366 .6 572 317 1.668 .469 -.738 -1.091 -1.091
11 1010 767 315 228 695 539 938 752 358 242 623 524 0 0 294 186 428 79 75 100 26 100 1234 1147 1.289 .776 .841 .799 .806 1.474 52 278 .707 .86 80 3730 9390 47 55 181 189 0 807 240 567 .816 792 552 1.225 .885 -.293 -.176 -.176
12 939 806 313 232 626 574 947 750 328 246 634 518 0 0 258 224 108 94 96 100 96 96 1200 1152 1.091 .917 .817 .933 .927 1.657 32 204 .918 .82 70 3860 9390 47 54 194 201 0 848 244 604 .965 789 545 1.036 .86 -.051 -.218 -.218
13 1065 1076 306 229 759 847 1090 1043 322 238 784 814 0 0 368 328 109 87 96 100 88 100 1606 1598 .896 1.116 1.038 1.255 1.202 1.766 52 254 1.075 .87 80 4010 9390 47 55 209 217 0 1133 241 892 1.175 1098 857 .851 1.093 .232 .128 .128
14 1817 1358 302 225 1515 1133 1812 1417 320 235 1510 1192 0 0 479 371 124 77 100 100 100 100 2648 2702 1.337 .748 .789 .748 .731 1.314 80 441 .714 .93 110 4150 9390 45 56 221 232 0 1429 237 1193 .787 1492 1255 1.27 .831 -.345 -.267 -.267
15 1024 830 299 237 725 593 1025 837 322 245 726 600 0 0 325 262 138 82 96 98 92 96 1318 1326 1.223 .818 .826 .839 .731 1.916 52 300 .756 .78 90 4300 9390 46 55 237 246 0 874 249 624 .861 881 632 1.161 .87 -.216 -.201 -.201
16 2191 2147 297 230 1894 1917 2230 2162 316 236 1933 1932 0 0 689 515 122 76 100 100 98 100 3811 3865 .988 1.012 .999 1.065 .995 1.452 80 420 .984 .94 110 4450 9390 45 56 251 262 0 2260 242 2018 1.065 2276 2034 .939 1.052 .091 .073 .073
17 1837 1767 298 218 1539 1549 1830 1882 305 226 1532 1664 0 0 576 502 83 71 100 100 100 100 3088 3196 .994 1.006 1.086 1.029 1.04 1.276 80 344 .977 .95 100 4600 9390 46 56 267 277 0 1860 229 1631 1.059 1981 1752 .944 1.143 .083 .193 .193
18 401 275 304 210 97 65 348 257 305 219 44 47 0 0 203 129 81 66 36 42 19 19 162 91 1.492 .67 1.068 .601 .531 3.733 52 235 .529 .49 80 4740 9380 46 54 282 290 -50 289 221 68 .705 271 49 1.418 1.124 -.504 .169
19 2394 2277 305 213 2089 2064 1934 2531 329 235 1629 2318 0 0 3435 882 235 196 92 93 90 93 4153 3947 1.012 .988 1.423 1.238 1.278 1.849 80 372 .311 .85 100 4890 9380 45 55 296 306 0 2397 224 2173 1.04 2664 2440 .962 1.498 .057 .583 .583
20 1264 1074 291 211 973 863 1303 1055 302 220 1012 844 0 0 439 274 89 74 100 100 100 100 1836 1856 1.127 .887 .834 .955 .93 1.558 52 301 .814 .87 90 5030 9380 45 54 310 319 0 1131 222 908 .934 1111 888 1.071 .878 -.099 -.188 -.188

Total number of rows: 43008

Table truncated, full table size 9918 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap