NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39899 Query DataSets for GSM39899
Status Public on Feb 21, 2005
Title Stomach, fundus 0878
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Stomach, fundus 0878
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26553.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
1 152 153 68 82 84 71 158 154 69 86 90 72 0 0 37 46 11 31 96 75 94 55 155 162 1.183 .845 .8 .708 .79 2.811 52 316 1.188 .55 80 1360 8390 39 47 8 16 0 138 74 64 .761 139 65 1.313 .721 -.393 -.472 -.393
2 128 154 65 81 63 73 129 146 66 84 64 65 0 0 23 64 10 31 100 76 96 53 136 129 .863 1.159 1.016 1.072 1.155 3.184 52 323 3.081 .46 90 1520 8390 38 47 23 32 0 139 73 66 1.044 132 59 .958 .915 .062 -.128 .062
3 527 594 66 85 461 509 562 590 67 90 496 505 0 0 178 173 11 31 100 100 100 100 970 1001 .906 1.104 1.018 1.162 1.087 1.679 52 264 1.049 .85 80 1660 8390 39 47 38 46 0 535 77 459 .995 532 455 1.005 .917 -.008 -.125 -.008
4 1650 2728 65 84 1585 2644 1731 2785 67 87 1666 2701 0 0 700 1154 10 28 100 100 100 100 4229 4367 .599 1.668 1.621 1.704 1.541 1.966 52 313 1.783 .88 90 1800 8390 38 47 51 60 0 2458 76 2382 1.503 2509 2433 .665 1.461 .588 .547 .588
5 192 262 65 80 127 182 214 261 67 85 149 181 0 0 77 101 10 31 96 98 92 90 309 330 .698 1.433 1.215 1.483 1.313 2.442 52 274 1.651 .67 80 1940 8390 39 47 66 74 0 236 72 164 1.291 235 163 .775 1.094 .369 .13 .369
6 108 166 66 91 42 75 111 162 68 95 45 71 0 0 25 39 9 34 87 87 84 53 117 116 .56 1.786 1.578 1.54 1.66 2.853 32 204 3.937 .41 70 2090 8390 39 46 81 88 0 150 82 68 1.609 146 64 .622 1.421 .686 .507 .686
7 190 149 66 93 124 56 196 140 67 96 130 47 0 0 47 44 10 33 96 71 94 36 180 177 2.214 .452 .362 .461 .439 2.82 52 264 .493 .45 80 2240 8390 39 47 96 104 0 134 84 50 .407 126 42 2.458 .326 -1.297 -1.618 -1.297
8 1269 1597 67 85 1202 1512 1291 1632 67 87 1224 1547 0 0 676 651 10 28 100 100 100 100 2714 2771 .795 1.258 1.264 1.444 1.231 2.028 52 333 1.151 .93 90 2380 8380 37 46 109 118 0 1439 77 1362 1.133 1470 1394 .882 1.139 .18 .187 .18
9 312 367 67 89 245 278 332 377 68 92 265 288 0 0 88 118 10 29 100 100 100 96 523 553 .881 1.135 1.087 1.101 1.196 1.742 52 243 1.206 .87 80 2530 8390 39 47 125 133 0 331 80 250 1.022 340 259 .978 .979 .032 -.03 .032
10 133 176 67 92 66 84 138 175 68 97 71 83 0 0 32 63 11 33 94 76 92 57 150 154 .786 1.273 1.169 1.264 1.408 3.319 52 264 2.633 .51 80 2670 8390 39 47 139 147 0 159 83 76 1.147 158 75 .872 1.053 .197 .075 .197
11 332 308 65 95 267 213 354 310 66 99 289 215 0 0 125 93 10 34 98 100 98 96 480 504 1.254 .798 .744 .869 .762 1.964 52 328 .796 .81 90 2820 8390 38 47 153 162 0 277 86 192 .719 279 194 1.391 .67 -.477 -.577 -.477
12 408 285 66 94 342 191 438 261 67 99 372 167 0 0 105 91 10 34 98 100 98 90 533 539 1.791 .558 .449 .552 .538 1.95 52 324 .589 .82 90 2970 8390 38 47 168 177 0 257 85 172 .503 235 150 1.988 .404 -.991 -1.306 -.991
13 218 206 67 95 151 111 235 205 68 98 168 110 0 0 66 66 10 34 93 87 93 68 262 278 1.36 .735 .655 .707 .688 2.678 32 190 .829 .7 70 3110 8400 40 47 183 190 0 186 86 100 .662 185 99 1.51 .59 -.595 -.762 -.595
14 115 153 66 98 49 55 119 144 67 103 53 46 0 0 24 40 9 31 93 68 93 43 104 99 .891 1.122 .868 .762 .84 2.853 32 176 2.748 .39 60 3250 8390 40 46 198 204 0 138 88 50 1.011 130 41 .989 .782 .016 -.355 .016
15 1140 1108 65 96 1075 1012 1180 1173 66 100 1115 1077 0 0 392 395 9 34 100 100 100 100 2087 2192 1.062 .941 .966 .973 .925 1.761 52 293 .96 .94 90 3410 8390 38 47 212 221 0 998 86 912 .848 1057 970 1.179 .87 -.238 -.201 -.238
16 383 520 65 89 318 431 432 550 66 95 367 461 0 0 138 196 9 32 100 95 98 92 749 828 .738 1.355 1.256 1.386 1.38 2.36 80 307 1.421 .87 100 3550 8390 38 48 226 236 0 468 80 388 1.221 495 415 .819 1.132 .288 .178 .288
17 82 142 65 99 17 43 85 137 66 104 20 38 0 0 18 43 9 35 62 51 50 23 60 58 .395 2.529 1.9 1.935 2.233 3.472 80 315 10.776 .21 100 3680 8380 37 47 239 249 -50 128 89 39 2.279 123 34 .439 1.712 .775 1.188
18 84 122 64 100 20 22 79 115 66 100 15 15 0 0 24 37 10 31 57 38 38 10 42 30 .909 1.1 1 1.561 1.341 3.751 80 331 11.236 .14 100 3830 8380 37 47 254 264 -50 110 90 20 .991 104 14 1.009 .901 -.151 -.013
19 179 231 67 95 112 136 188 231 67 98 121 136 0 0 51 66 10 31 96 98 94 90 248 257 .824 1.214 1.124 1.19 1.139 2.131 52 278 1.398 .77 80 3980 8390 39 47 270 278 0 208 86 123 1.094 208 123 .914 1.013 .13 .018 .13
20 88 149 71 110 17 39 90 160 72 116 19 50 0 0 27 46 12 37 66 58 41 33 56 69 .436 2.294 2.632 1.921 1.878 2.348 12 104 6.954 .23 50 4120 8380 39 44 285 290 0 134 99 35 2.067 144 45 .484 2.371 1.047 1.245 1.047

Total number of rows: 43008

Table truncated, full table size 8837 Kbytes.




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