NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39912 Query DataSets for GSM39912
Status Public on Feb 21, 2005
Title Lung 1356
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lung 1356
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24456.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 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 GPL1823
Series (1)
GSE2193 Normal_human_tissues

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 same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 432 229 242 143 190 86 435 221 248 147 193 78 0 0 125 82 54 41 90 67 78 50 276 271 2.209 .453 .404 .476 .495 2.479 52 302 .342 .46 80 1480 7550 23 31 36 44 0 136 85 51 .269 132 46 3.712 .241 -1.892 -2.056 -1.892
2 422 210 260 151 162 59 420 216 265 160 160 65 0 0 64 70 62 46 90 65 68 34 221 225 2.746 .364 .406 .429 .493 2.625 32 203 .282 .38 70 1610 7570 25 32 49 56 0 125 90 35 .217 129 39 4.613 .242 -2.206 -2.048 -2.206
3 908 2118 271 167 637 1951 957 2120 275 173 686 1953 0 0 267 846 60 47 92 100 92 100 2588 2639 .326 3.063 2.847 3.165 3.129 1.853 52 338 3.68 .87 90 1760 7550 22 31 63 72 0 1261 99 1161 1.823 1262 1163 .549 1.695 .866 .761 .866
4 3785 10289 269 169 3516 10120 3737 10699 353 234 3468 10530 0 0 1423 5260 572 455 96 100 94 96 13636 13998 .347 2.878 3.036 2.616 3.076 2.069 52 314 3.385 .87 90 1900 7550 22 31 77 86 0 6124 101 6024 1.713 6368 6268 .584 1.807 .777 .854 .777
5 514 1003 260 156 254 847 544 1004 372 244 284 848 0 0 217 486 663 528 1 67 0 36 1101 1132 .3 3.335 2.986 2.915 3.254 2.263 52 233 .811 .85 80 2040 7560 24 32 92 100 0 597 93 504 1.985 598 505 .504 1.777 .989 .83 .989
6 370 211 278 175 92 36 365 201 284 180 87 26 0 0 114 67 65 54 55 31 36 12 128 113 2.556 .391 .299 .421 .479 3.462 80 404 .343 .29 100 2180 7550 22 32 105 115 0 126 104 21 .233 120 15 4.293 .178 -2.102 -2.491 -2.102
7 644 6440 307 192 337 6248 648 6601 308 199 341 6409 0 0 176 2056 64 54 90 100 86 100 6585 6750 .054 18.54 18.795 18.143 16.6 1.789 52 249 19.346 .76 90 2340 7560 23 32 121 130 0 3833 114 3719 11.036 3929 3815 .091 11.187 3.464 3.484 3.464
8 4652 8672 316 202 4336 8470 4474 8857 320 207 4158 8655 0 0 1615 3832 60 49 100 100 100 100 12806 12813 .512 1.953 2.082 1.841 1.981 1.442 52 274 2.131 .93 90 2480 7550 22 31 135 144 0 5162 120 5042 1.163 5272 5152 .86 1.239 .218 .309 .218
9 701 2416 279 192 422 2224 739 2612 287 203 460 2420 0 0 300 976 71 69 80 100 73 100 2646 2880 .19 5.27 5.261 6.492 5.462 2.028 52 300 4.93 .86 80 2620 7560 24 32 150 158 0 1438 114 1324 3.137 1555 1440 .319 3.131 1.649 1.647 1.649
10 645 640 322 250 323 390 655 640 326 258 333 390 0 0 207 216 76 63 84 90 78 87 713 723 .828 1.207 1.171 1.189 1.167 3.189 32 144 1.057 .69 60 2780 7560 25 31 167 173 0 381 149 232 .719 381 232 1.391 .697 -.477 -.521 -.477
11 945 1079 358 238 587 841 935 1046 359 239 577 808 0 0 380 441 64 58 90 96 88 96 1428 1385 .698 1.433 1.4 1.62 1.408 3.139 52 280 1.379 .86 80 2910 7560 24 32 179 187 0 642 142 501 .853 623 481 1.173 .834 -.23 -.263 -.23
12 1263 1382 351 223 912 1159 1253 1351 355 228 902 1128 0 0 395 418 69 53 98 100 96 100 2071 2030 .787 1.271 1.251 1.383 1.25 1.73 52 297 1.21 .91 80 3060 7560 24 32 194 202 0 823 133 690 .756 804 671 1.322 .744 -.403 -.426 -.403
13 783 960 326 210 457 750 803 1017 326 211 477 807 0 0 229 307 65 52 90 100 87 96 1207 1284 .609 1.641 1.692 1.834 1.654 1.917 32 210 1.595 .85 70 3210 7560 24 31 209 216 0 571 125 446 .977 605 480 1.024 1.007 -.034 .01 -.034
14 585 428 340 212 245 216 590 433 347 217 250 221 0 0 187 131 70 50 81 90 78 78 461 471 1.134 .882 .884 .804 .808 2.468 32 211 .706 .61 70 3360 7550 23 30 224 231 0 255 126 129 .525 258 132 1.906 .526 -.93 -.926 -.93
15 4730 7474 346 225 4384 7249 4981 7586 358 236 4635 7361 0 0 2239 2651 128 81 100 100 100 100 11633 11996 .605 1.654 1.588 1.839 1.609 1.797 52 280 1.545 .93 90 3490 7560 23 32 236 245 0 4449 134 4315 .984 4515 4382 1.016 .945 -.023 -.081 -.023
16 1635 2645 330 222 1305 2423 1698 2697 344 231 1368 2475 0 0 389 726 126 64 100 100 100 100 3728 3843 .539 1.857 1.809 1.811 1.851 1.508 52 307 1.826 .92 90 3640 7560 23 32 251 260 0 1574 132 1442 1.105 1605 1473 .905 1.077 .144 .107 .144
17 602 294 370 242 232 52 644 292 374 248 274 50 0 0 189 78 79 51 84 50 71 25 284 324 4.462 .224 .182 .233 .249 4.112 32 156 .103 .2 60 3800 7550 24 30 269 275 0 175 144 31 .133 174 30 7.495 .109 -2.906 -3.203 -2.906
18 415 232 366 240 49 -8 406 229 377 309 40 -11 0 0 118 63 176 799 13 0 1 0 41 29 null null null .583 .582 3.556 80 376 .183 .18 100 3930 7540 21 31 280 290 -50 138 143 -5 null 136 null null null null null
19 889 1002 378 238 511 764 926 977 377 237 548 739 0 0 281 396 67 47 90 100 90 96 1275 1287 .669 1.495 1.349 1.442 1.549 1.7 32 196 1.472 .87 70 4080 7560 24 31 296 303 0 596 142 455 .89 582 440 1.124 .803 -.168 -.317 -.168
20 542 271 371 241 171 30 557 274 370 247 186 33 0 0 147 59 73 60 81 25 65 6 201 219 5.7 .175 .177 .283 .274 2.637 32 165 .178 .28 60 4230 7540 23 29 312 318 0 161 143 18 .104 163 20 9.576 .106 -3.259 -3.243 -3.259

Total number of rows: 43008

Table truncated, full table size 9394 Kbytes.




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