NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39906 Query DataSets for GSM39906
Status Public on Feb 21, 2005
Title Adrenal 1354
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Adrenal 1354
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24160.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
1 528 402 252 164 276 238 554 398 253 166 302 234 0 0 173 138 49 49 88 94 86 82 514 536 1.16 .862 .775 .7 .751 2.384 52 296 .77 .73 80 1420 7590 59 67 54 62 0 253 103 150 .542 250 147 1.844 .487 -.883 -1.037 -.883
2 439 244 254 163 185 81 457 254 257 165 203 91 0 0 134 59 49 48 80 73 76 42 266 294 2.284 .438 .448 .416 .434 3.115 52 300 .227 .3 90 1570 7590 58 67 68 77 0 153 103 51 .275 160 57 3.631 .282 -1.861 -1.827 -1.861
3 1156 2612 254 169 902 2443 1126 2576 257 170 872 2407 0 0 460 1200 51 47 96 100 96 100 3345 3279 .369 2.708 2.76 2.638 2.699 1.451 80 395 2.801 .95 100 1710 7590 58 68 82 92 0 1643 106 1536 1.703 1620 1514 .587 1.736 .768 .796 .768
4 3680 11973 256 175 3424 11798 3848 13151 259 178 3592 12976 0 0 1669 5745 51 52 100 100 100 100 15222 16568 .29 3.446 3.612 3.553 3.337 1.42 52 313 3.532 .97 90 1860 7590 58 67 97 106 0 7530 110 7420 2.167 8271 8161 .461 2.272 1.116 1.184 1.116
5 597 1300 256 171 341 1129 582 1212 261 177 326 1041 0 0 209 531 52 53 86 100 84 100 1470 1367 .302 3.311 3.193 3.607 2.98 2.038 52 314 3.307 .88 90 2000 7600 59 68 111 120 0 818 108 710 2.082 762 655 .48 2.008 1.058 1.006 1.058
6 459 360 260 180 199 180 477 371 260 178 217 191 0 0 146 76 51 51 84 93 78 90 379 408 1.106 .905 .88 .864 .925 1.544 32 218 .841 .66 70 2150 7600 60 67 127 134 0 226 113 113 .569 233 120 1.758 .554 -.814 -.853 -.814
7 665 1520 245 175 420 1345 717 1618 249 175 472 1443 0 0 218 568 54 51 92 100 88 100 1765 1915 .312 3.202 3.057 3.179 2.942 1.511 52 298 3.306 .9 90 2290 7590 58 67 140 149 0 956 110 846 2.014 1018 908 .497 1.923 1.01 .943 1.01
8 2697 9048 241 172 2456 8876 2620 9089 243 176 2379 8917 0 0 1562 4925 48 54 96 100 92 100 11332 11296 .277 3.614 3.748 3.955 3.493 1.91 80 346 3.592 .95 100 2450 7600 59 69 156 166 0 5691 108 5582 2.273 5716 5608 .44 2.357 1.185 1.237 1.185
9 1140 3594 247 161 893 3433 1244 3921 248 170 997 3760 0 0 410 983 50 56 96 100 93 100 4326 4757 .26 3.844 3.771 4.553 3.816 2.235 32 196 3.756 .89 70 2590 7600 60 67 171 178 0 2260 101 2159 2.418 2466 2365 .414 2.372 1.274 1.246 1.274
10 428 368 239 164 189 204 432 372 239 168 193 208 0 0 116 82 45 49 84 96 81 93 393 401 .926 1.079 1.078 1.162 1.05 2.51 32 212 .957 .64 70 2740 7600 60 67 186 193 0 231 103 128 .679 234 131 1.473 .678 -.559 -.561 -.559
11 958 1758 246 175 712 1583 933 1769 249 181 687 1594 0 0 366 608 49 55 96 100 90 100 2295 2281 .45 2.223 2.32 2.528 2.282 1.611 52 270 2.165 .94 80 2880 7600 60 68 200 208 0 1106 110 996 1.398 1113 1003 .715 1.459 .484 .545 .484
12 1068 1034 248 185 820 849 1073 1000 253 189 825 815 0 0 392 409 51 58 100 98 98 96 1669 1640 .966 1.035 .988 1.024 1.072 1.648 52 312 1.056 .93 90 3030 7590 58 67 214 223 0 650 116 534 .651 629 513 1.536 .621 -.619 -.687 -.619
13 752 1610 241 186 511 1424 762 1784 244 188 521 1598 0 0 304 840 46 53 94 98 94 96 1935 2119 .359 2.787 3.067 2.517 2.741 1.996 52 275 2.885 .95 80 3170 7590 59 67 229 237 0 1013 117 896 1.753 1122 1005 .571 1.929 .81 .948 .81
14 402 1012 260 197 142 815 405 1076 278 255 145 879 0 0 130 318 111 421 65 84 31 56 957 1024 .174 5.739 6.062 5.847 5.479 1.835 32 221 4.891 .72 70 3320 7600 60 67 244 251 0 636 124 513 3.61 677 553 .277 3.813 1.852 1.931 1.852
15 2621 7348 260 213 2361 7135 2850 8060 273 268 2590 7847 0 0 1013 2818 104 404 100 100 96 96 9496 10437 .331 3.022 3.03 3.141 3.122 2.141 52 311 3.194 .93 90 3480 7600 59 68 259 268 0 4621 134 4487 1.901 5069 4935 .526 1.905 .926 .93 .926
16 1097 8883 268 210 829 8673 1206 9917 269 214 938 9707 0 0 477 4353 55 55 88 100 86 100 9502 10645 .096 10.462 10.349 10.167 10.06 1.741 80 369 10.726 .93 100 3600 7600 59 69 271 281 0 5587 132 5455 6.58 6237 6105 .152 6.509 2.718 2.702 2.718
17 411 347 272 206 139 141 413 356 271 209 141 150 0 0 119 95 50 52 82 80 65 69 280 291 .986 1.014 1.064 .926 .991 2.65 52 270 .859 .55 80 3760 7600 60 68 288 296 0 218 130 89 .638 224 94 1.567 .669 -.648 -.58 -.648
18 415 348 258 205 157 143 460 343 262 206 202 138 0 0 123 98 46 53 84 84 65 62 300 340 1.098 .911 .683 .845 .83 2.085 32 160 .835 .63 60 3900 7600 61 67 303 309 0 219 129 90 .573 216 87 1.746 .43 -.804 -1.219 -.804
19 702 1006 263 202 439 804 694 1003 266 204 431 801 0 0 288 498 50 53 92 100 88 98 1243 1232 .546 1.831 1.858 1.855 1.842 1.657 52 283 1.87 .91 80 4040 7600 60 68 316 324 0 633 127 506 1.152 631 504 .868 1.169 .204 .225 .204
20 426 377 274 189 152 188 457 380 274 195 183 191 0 0 126 100 53 52 75 87 75 78 340 374 .809 1.237 1.044 1.013 1.052 1.986 32 156 1.045 .62 60 4190 7600 61 67 332 338 0 237 119 118 .778 239 120 1.286 .656 -.362 -.607 -.362

Total number of rows: 43008

Table truncated, full table size 9389 Kbytes.




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