NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM40005 Query DataSets for GSM40005
Status Public on Feb 21, 2005
Title RNA_DNA Liver FT560 Tissue
Sample type mixed
 
Channel 1
Source name Cy3 - Normal female genomic DNA
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name Cy5 - Liver FT560 mRNA
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/23455.gif
 
Submission date Jan 26, 2005
Last update date Jun 17, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
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 GPL1827
Series (2)
GSE2193 Normal_human_tissues
GSE2194 Normal_human_tissues_genomic_controls

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
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

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 VALUE LOG_RAT2N_MEDIAN
1 516 744 188 175 328 569 526 781 190 180 338 606 0 0 105 241 41 58 100 100 100 98 897 944 .576 1.735 1.793 1.633 1.832 1.75 80 405 2.011 .83 100 1790 9550 26 36 26 36 0 506 119 387 1.18 531 412 .847 1.22 .239 .286
2 697 205 201 146 496 59 710 193 201 154 509 47 0 0 121 60 42 52 100 46 100 26 555 556 8.407 .119 .092 .118 .137 2.362 80 331 .112 .42 100 1940 9550 26 36 41 51 0 139 99 40 .081 131 32 12.358 .063 -3.627 -3.993
3 534 1574 202 158 332 1416 539 1632 202 213 337 1474 0 0 98 444 42 226 100 100 98 98 1748 1811 .234 4.265 4.374 4.301 4.291 1.464 80 388 4.755 .85 110 2080 9550 25 36 54 65 0 1071 107 963 2.901 1110 1003 .345 2.975 1.537 1.573
4 536 10249 205 192 331 10057 561 10672 207 347 356 10480 0 0 143 2663 42 341 96 100 95 100 10388 10836 .033 30.384 29.438 31.35 30.138 1.419 80 358 29.193 .91 100 2220 9550 26 36 69 79 0 6972 131 6841 20.669 7260 7129 .048 20.026 4.369 4.324
5 752 402 213 185 539 217 779 418 216 264 566 233 0 0 141 95 46 246 100 46 100 0 756 799 2.484 .403 .412 .399 .417 1.629 52 305 .654 .29 90 2370 9540 25 34 84 93 0 273 126 148 .274 284 159 3.651 .28 -1.868 -1.836
6 557 300 213 186 344 114 561 291 216 193 348 105 0 0 104 88 51 65 96 76 96 40 458 453 3.018 .331 .302 .319 .376 2.119 52 283 .337 .47 90 2520 9550 26 35 99 108 0 204 127 78 .225 198 71 4.436 .205 -2.149 -2.285
7 452 295 212 203 240 92 481 283 214 207 269 80 0 0 123 82 39 65 90 59 86 25 332 349 2.609 .383 .297 .371 .387 3.063 120 456 .392 .48 120 2670 9550 25 37 113 125 0 201 138 63 .261 193 54 3.835 .202 -1.939 -2.305
8 994 8814 208 195 786 8619 1073 9431 212 199 865 9236 0 0 355 3799 40 59 98 100 96 100 9405 10101 .091 10.966 10.677 11.372 11.163 1.605 120 460 11.582 .94 120 2810 9550 25 37 127 139 0 5996 133 5863 7.46 6416 6283 .134 7.264 2.899 2.861
9 903 1239 212 180 691 1059 920 1262 215 182 708 1082 0 0 228 329 40 55 100 100 100 100 1750 1790 .653 1.533 1.528 1.548 1.423 1.37 80 322 1.572 .93 100 2960 9550 26 36 143 153 0 843 122 720 1.043 859 736 .959 1.04 .06 .056
10 716 271 218 158 498 113 706 271 222 172 488 113 0 0 167 69 52 69 100 71 98 28 611 601 4.407 .227 .232 .225 .245 1.899 52 281 .159 .46 90 3100 9540 25 34 157 166 0 184 107 77 .154 184 77 6.478 .158 -2.696 -2.666
11 1799 2651 208 154 1591 2497 1869 2806 211 167 1661 2652 0 0 434 719 52 78 100 100 100 100 4088 4313 .637 1.569 1.597 1.564 1.542 1.324 80 413 1.674 .94 110 3260 9550 25 36 172 183 0 1803 105 1699 1.068 1909 1804 .937 1.086 .094 .119
12 713 2142 206 165 507 1977 745 2282 207 176 539 2117 0 0 180 784 46 73 100 100 100 100 2484 2656 .256 3.899 3.928 3.835 3.787 1.635 52 293 4.535 .86 90 3400 9540 25 34 187 196 0 1457 112 1345 2.653 1552 1440 .377 2.672 1.407 1.418
13 1147 1263 214 197 933 1066 1165 1279 217 201 951 1082 0 0 433 405 45 64 98 100 98 100 1999 2033 .875 1.143 1.138 1.257 1.096 1.677 52 293 1.081 .91 90 3540 9540 25 34 201 210 0 859 134 725 .777 870 736 1.287 .774 -.364 -.37
14 610 273 224 209 386 64 621 254 223 210 397 45 0 0 151 82 39 66 100 44 100 17 450 442 6.031 .166 .113 .176 .225 3.01 52 256 .171 .36 80 3690 9540 26 34 217 225 0 186 142 44 .113 173 31 8.866 .077 -3.148 -3.697
15 3172 4858 213 194 2959 4664 3272 4960 216 204 3059 4766 0 0 754 1210 50 81 100 100 100 100 7623 7825 .634 1.576 1.558 1.576 1.515 1.301 80 416 1.611 .95 110 3840 9550 25 36 230 241 0 3305 132 3173 1.072 3374 3242 .933 1.06 .101 .084
16 1249 7063 207 190 1042 6873 1264 7240 210 196 1057 7050 0 0 349 1862 51 60 100 100 100 100 7915 8107 .152 6.596 6.67 6.843 6.464 1.357 80 340 6.712 .95 100 3980 9550 26 36 245 255 0 4805 129 4676 4.487 4925 4796 .223 4.537 2.166 2.182
17 695 620 206 196 489 424 737 626 208 202 531 430 0 0 155 178 40 62 100 98 100 96 913 961 1.153 .867 .81 .833 .852 1.663 52 276 .91 .84 90 4120 9550 26 35 259 268 0 422 133 288 .59 426 293 1.695 .551 -.762 -.86
18 621 207 210 196 411 11 608 204 212 201 398 8 0 0 150 73 41 62 100 23 96 5 422 406 37.364 .027 .02 .105 .117 2.643 52 275 .061 .09 90 4270 9540 25 34 274 283 0 141 133 7 .018 139 5 54.925 .014 -5.779 -6.192
19 653 2275 212 195 441 2080 682 2306 213 200 470 2111 0 0 167 896 40 60 98 100 97 100 2521 2581 .212 4.717 4.491 4.606 4.373 1.696 120 481 5.354 .88 120 4420 9540 24 36 288 300 0 1548 133 1415 3.209 1569 1436 .312 3.055 1.682 1.611
20 651 310 217 195 434 115 652 313 223 205 435 118 0 0 164 105 56 62 98 67 96 48 549 553 3.774 .265 .271 .306 .354 2.364 52 219 .243 .49 80 4570 9540 26 34 305 313 0 211 133 78 .18 213 80 5.548 .185 -2.472 -2.438

Total number of rows: 43008

Table truncated, full table size 9184 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap