NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM35651 Query DataSets for GSM35651
Status Public on May 27, 2005
Title array-CGH - AOA1
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name AOA1
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-05/51561.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 32.67; Parameter Scan Time = 17:15:40; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 85362; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 32.67; Parameter Scan Time = 17:15:40; Parameter PMT Volts = 720; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 154840; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
 
Submission date Nov 19, 2004
Last update date May 29, 2005
Contact name Markus Bredel
E-mail(s) mbredel@stanford.edu
Phone 650-498-6012
Organization name Stanford University School of Medicine
Street address
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1715
Series (1)
GSE1991 Array-CGH in human glial brain tumors

Data table header descriptions
ID_REF ID_REF
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
VALUE 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
LOG_RAT2N_MEDIAN 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
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

Data table
ID_REF CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN 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
1 670 387 283 .706 641 254 1.416 .606 -.502 -.723 566 641 165 370 401 271 584 613 168 377 419 243 0 0 95 137 30 93 100 96 100 70 672 662 1.48 .676 .58 .605 .578 1.924 57 296 .828 .67 90 1730 6000 43 52 36 45 0
2 996 388 608 .734 968 580 1.362 .651 -.445 -.62 992 953 164 371 828 582 1055 926 167 382 891 555 0 0 229 172 39 105 100 100 100 97 1410 1446 1.423 .703 .623 .707 .699 1.515 47 236 .689 .88 80 1870 5990 43 51 51 59 0
3 944 391 553 .595 931 540 1.681 .546 -.749 -.874 1095 903 166 374 929 529 1156 891 168 383 990 517 0 0 365 258 35 104 100 100 100 94 1458 1507 1.756 .569 .522 .577 .529 1.959 68 347 .548 .81 100 2020 6000 43 53 65 75 0
4 836 390 446 .674 838 448 1.484 .669 -.569 -.58 831 800 169 373 662 427 839 802 171 386 670 429 0 0 139 138 30 100 100 100 100 94 1089 1099 1.55 .645 .64 .624 .64 1.567 38 169 .641 .81 70 2160 5990 43 50 80 87 0
5 1473 397 1076 1.107 1500 1103 .903 1.1 .147 .138 1135 1410 163 380 972 1030 1166 1436 165 383 1003 1056 0 0 286 311 30 96 100 100 100 98 2002 2059 .944 1.06 1.053 1.072 1.033 1.543 73 372 1.123 .92 100 2310 5990 42 52 94 104 0
6 747 397 350 .645 737 340 1.551 .613 -.633 -.706 703 715 160 380 543 335 714 705 164 382 554 325 0 0 112 157 33 100 100 96 100 90 878 879 1.621 .617 .587 .54 .582 2.211 31 139 .69 .71 60 2460 6000 45 51 111 117 0
7 2202 394 1808 1.586 1232 838 .631 1.103 .665 .141 1310 2107 170 377 1140 1730 930 1179 172 384 760 802 0 0 1658 3841 35 96 100 100 100 100 2870 1562 .659 1.518 1.055 1.117 1.139 1.45 64 259 2.228 .94 90 2610 5990 42 51 124 133 0
8 641 397 243 .247 620 223 4.054 .242 -2.019 -2.049 1159 613 172 380 987 233 1093 593 175 394 921 213 0 0 338 210 33 100 100 71 100 52 1220 1134 4.236 .236 .231 .185 .236 2.953 59 247 .22 .57 90 2750 5990 42 51 138 147 0
9 659 440 219 .415 649 209 2.411 .376 -1.269 -1.412 719 631 190 421 529 210 746 621 224 435 556 200 0 0 86 93 108 131 100 81 100 31 739 756 2.519 .397 .36 .345 .371 1.945 22 139 .367 .44 60 2890 6000 45 51 154 160 0
10 1028 444 584 .636 1007 563 1.573 .626 -.654 -.675 1110 984 191 425 919 559 1090 964 205 436 899 539 0 0 165 184 67 123 100 100 100 96 1478 1438 1.644 .608 .6 .579 .588 1.385 53 223 .589 .86 80 3040 5990 43 51 168 176 0
11 695 422 273 .665 680 258 1.503 .603 -.588 -.73 593 665 183 404 410 261 611 651 187 413 428 247 0 0 85 121 38 103 100 94 100 58 671 675 1.571 .637 .577 .579 .596 1.834 56 232 .779 .69 80 3190 5990 43 51 183 191 0
12 709 429 280 .588 704 275 1.7 .56 -.765 -.837 658 679 182 411 476 268 673 674 187 413 491 263 0 0 103 113 37 101 100 96 100 71 744 754 1.776 .563 .536 .523 .534 1.736 53 231 .616 .71 80 3330 5990 43 51 197 205 0
13 858 425 433 .702 819 394 1.424 .647 -.51 -.628 799 821 183 407 616 414 792 784 190 417 609 377 0 0 102 155 40 113 100 100 100 91 1030 986 1.488 .672 .619 .632 .628 1.506 61 256 .712 .78 90 3480 5990 42 51 211 220 0
14 1271 429 841 1.058 1249 819 .945 1.005 .081 .007 983 1216 188 411 795 805 1003 1195 196 426 815 784 0 0 144 196 40 126 100 100 100 100 1600 1599 .988 1.013 .962 1.002 1.013 1.314 65 265 1.042 .88 90 3630 5980 41 50 226 235 0
15 634 404 230 .774 652 248 1.292 .86 -.37 -.218 490 607 193 387 297 220 481 624 199 401 288 237 0 0 53 94 35 107 100 87 100 62 517 525 1.35 .741 .823 .639 .841 2.175 24 161 .783 .51 70 3760 5990 43 50 240 247 0
16 1746 416 1330 .93 1739 1323 1.076 .886 -.105 -.175 1628 1671 197 398 1431 1273 1690 1664 214 424 1493 1266 0 0 309 291 60 142 100 100 100 100 2704 2759 1.124 .89 .848 .892 .892 1.281 56 235 .868 .95 80 3920 5990 43 51 256 264 0
17 1310 487 823 1.033 1299 812 .968 1.009 .047 .012 1015 1254 218 466 797 788 1023 1243 229 478 805 777 0 0 168 201 70 141 100 100 100 100 1585 1582 1.011 .989 .965 .98 .987 1.311 61 249 1.027 .92 90 4070 5990 42 51 270 279 0
18 1005 480 526 .591 997 517 1.693 .588 -.76 -.767 1111 962 221 459 890 503 1101 954 226 474 880 495 0 0 118 152 64 128 100 100 100 96 1393 1375 1.769 .565 .563 .545 .562 1.329 51 218 .573 .83 80 4210 5980 42 50 285 293 0
19 3313 447 2866 1.14 3194 2747 .877 1.101 .189 .139 2719 3171 204 428 2515 2743 2698 3057 211 438 2494 2629 0 0 475 597 52 120 100 100 100 100 5258 5123 .917 1.091 1.054 1.087 1.093 1.174 69 259 1.078 .98 90 4350 5980 41 50 298 307 0
20 957 414 543 .955 960 546 1.047 .971 -.067 -.043 750 916 181 396 569 520 744 919 185 409 563 523 0 0 130 171 40 112 100 100 100 98 1089 1086 1.094 .914 .929 .886 .891 1.473 61 250 .931 .84 90 4510 5980 41 50 314 323 0

Total number of rows: 41664

Table truncated, full table size 9503 Kbytes.




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