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Sample GSM81479 Query DataSets for GSM81479
Status Public on Nov 03, 2005
Title GC (LAM cells)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name GC (LAM cells)
Organism Homo sapiens
Characteristics GC (LAM cells)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19051.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 02, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3039
Series (2)
GSE3547 Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines
GSE3921 Embryonic stem cells and pluripotent germ cell tumors

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 1615 1860 290 198 1325 1662 1587 1634 305 218 1297 1436 0 0 760 1108 132 131 96 98 94 92 2987 2733 .797 1.254 1.107 1.171 1.226 1.53 52 297 1.316 .96 80 1760 8920 136 144 80 88 0 1632 174 1458 1.1 1433 1260 .909 .971 .138 -.042
2 2424 2167 288 200 2136 1967 1927 1411 297 207 1639 1211 0 0 1960 2078 65 68 100 96 100 96 4103 2850 1.086 .921 .739 .816 .945 1.755 32 136 1.002 .95 60 1910 8930 138 144 96 102 -100 1901 175 1725 .808 1238 1062 1.238 .648 -.308 -.626
3 15571 39675 281 210 15290 39465 16745 41521 295 223 16464 41311 0 0 5292 12710 82 100 100 100 100 100 54755 57775 .387 2.581 2.509 2.658 2.546 1.278 80 332 2.582 .98 110 2050 8910 133 144 107 118 0 34803 184 34618 2.264 36422 36238 .442 2.201 1.179 1.138
4 854 1043 272 202 582 841 317 308 282 210 45 106 0 0 1569 2049 65 74 45 52 28 40 1423 151 .692 1.445 2.356 1.858 2.016 3.454 80 255 1.331 .98 100 2160 8910 134 144 119 129 -50 915 177 738 1.268 270 93 .789 2.066 .342 1.047
5 6170 6699 278 195 5892 6504 6662 7474 279 203 6384 7279 0 0 2144 2437 59 76 100 100 100 100 12396 13663 .906 1.104 1.14 1.113 1.091 1.241 80 277 1.104 .98 100 2300 8910 134 144 133 143 0 5876 171 5705 .968 6556 6385 1.033 1 -.046 0
6 634 718 277 188 357 530 291 250 281 212 14 62 0 0 1050 1414 64 129 33 32 26 22 887 76 .674 1.485 4.429 2.006 1.551 3.695 80 295 1.381 .96 100 2430 8910 134 144 146 156 -50 630 165 465 1.302 219 54 .768 3.885 .381 1.958
7 7028 8312 280 188 6748 8124 7194 8186 287 210 6914 7998 0 0 2517 3084 66 129 100 100 100 100 14872 14912 .831 1.204 1.157 1.234 1.166 1.41 80 298 1.207 .98 100 2580 8910 134 144 161 171 0 7291 165 7126 1.056 7181 7016 .947 1.015 .079 .021
8 3208 1132 284 194 2924 938 3362 1007 292 209 3078 813 0 0 1112 611 71 85 97 97 97 90 3862 3891 3.117 .321 .264 .252 .315 1.973 80 311 .345 .9 100 2710 8910 134 144 174 184 0 993 170 823 .281 883 713 3.554 .232 -1.829 -2.11
9 4187 5134 281 203 3906 4931 3726 5103 290 217 3445 4900 0 0 2408 2740 78 70 100 100 100 100 8837 8345 .792 1.262 1.422 1.339 1.304 1.423 32 161 1.201 .98 70 2850 8930 137 144 189 196 0 4504 178 4325 1.107 4476 4298 .903 1.248 .147 .319
10 870 1198 291 207 579 991 842 1053 294 221 551 846 0 0 297 571 60 71 96 98 95 96 1570 1397 .584 1.712 1.535 1.646 1.642 1.501 80 310 1.79 .93 100 2980 8910 134 144 201 211 0 1051 182 869 1.501 924 742 .666 1.347 .586 .43
11 12754 53782 293 195 12461 53587 12889 56866 298 207 12596 56671 0 21 3855 12402 81 78 100 100 100 100 66048 69267 .233 4.3 4.499 4.503 4.25 1.357 80 288 4.225 .98 100 3120 8910 134 144 215 225 0 47177 171 47006 3.772 49882 49711 .265 3.947 1.915 1.981
12 3020 5230 294 198 2726 5032 3223 5413 298 207 2929 5215 0 0 1225 2004 87 79 100 100 100 100 7758 8144 .542 1.846 1.78 1.942 1.885 1.257 52 244 1.813 .98 90 3260 8910 134 143 229 238 0 4588 174 4414 1.619 4748 4575 .618 1.562 .695 .643
13 1706 4592 285 199 1421 4393 1654 4654 294 218 1369 4455 0 0 581 1441 72 112 98 100 97 100 5814 5824 .323 3.091 3.254 3.159 3.06 1.31 80 333 3.056 .95 110 3400 8910 133 144 242 253 0 4028 175 3854 2.712 4082 3908 .369 2.855 1.439 1.513
14 3855 4008 297 196 3558 3812 3768 4115 306 204 3471 3919 0 0 1346 1514 68 64 100 100 98 100 7370 7390 .933 1.071 1.129 1.087 1.052 1.364 80 298 1.076 .98 100 3540 8900 133 143 257 267 0 3516 172 3344 .94 3610 3438 1.064 .99 -.09 -.014
15 2535 3411 323 202 2212 3209 2237 3110 327 210 1914 2908 0 0 1728 2352 67 63 100 96 100 96 5421 4822 .689 1.451 1.519 1.548 1.491 1.65 32 108 1.428 .98 60 3660 8900 135 141 271 277 -100 2992 177 2815 1.273 2728 2551 .786 1.333 .348 .414
16 461 371 290 189 171 182 314 267 296 201 24 78 0 0 685 337 69 74 36 50 21 31 353 102 .94 1.064 3.25 1.653 1.344 3.461 80 325 .474 .79 100 3790 8900 133 143 282 292 -50 325 166 160 .934 234 68 1.071 2.851 -.099 1.511
17 2446 3166 295 199 2151 2967 2597 2953 303 214 2302 2754 0 0 840 1207 73 81 97 100 97 100 5118 5056 .725 1.379 1.196 1.435 1.328 1.706 80 274 1.396 .95 100 3940 8900 133 143 297 307 0 2777 175 2603 1.21 2590 2416 .826 1.049 .275 .07
18 2209 996 295 195 1914 801 2335 986 301 215 2040 791 0 0 649 348 68 99 96 98 96 97 2715 2831 2.39 .418 .388 .412 .396 1.724 80 259 .405 .91 100 4070 8900 133 143 310 320 0 874 171 703 .367 865 694 2.724 .34 -1.446 -1.556
19 1085 692 303 209 782 483 1107 699 312 219 804 490 0 0 357 263 72 94 97 96 95 88 1265 1294 1.619 .618 .609 .584 .59 1.679 80 287 .621 .84 100 4210 8890 132 142 324 334 0 607 183 424 .542 613 430 1.846 .535 -.884 -.903
20 5807 10149 313 211 5494 9938 5880 9940 321 222 5567 9729 0 0 1454 2972 79 82 100 100 98 100 15432 15296 .553 1.809 1.748 1.83 1.732 1.3 80 300 1.839 .98 100 4350 8890 132 142 338 348 0 8903 185 8718 1.587 8719 8534 .63 1.533 .666 .616

Total number of rows: 44544

Table truncated, full table size 10119 Kbytes.




Supplementary data files not provided
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