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Sample GSM81469 Query DataSets for GSM81469
Status Public on Nov 03, 2005
Title GC (SNU 16 cells)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SNU 16 cells
Organism Homo sapiens
Characteristics SNU 16 cells
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15413.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 1033 1680 172 100 861 1580 1023 1672 177 104 851 1572 0 0 307 716 39 31 100 100 100 100 2441 2423 .545 1.835 1.847 1.735 1.844 1.526 52 275 2.025 .92 80 1650 7950 31 39 129 137 0 1768 105 1663 1.932 1760 1655 .518 1.944 .95 .959
2 941 2261 173 102 768 2159 771 1424 176 107 598 1322 0 0 735 2388 38 34 100 100 100 100 2927 1920 .356 2.811 2.211 2.561 2.58 1.665 32 137 3.18 .95 70 1790 7960 32 39 143 150 0 2380 107 2273 2.959 1499 1392 .338 2.327 1.565 1.219
3 7730 22150 176 97 7554 22053 8569 23649 176 102 8393 23552 0 0 2465 6193 34 33 100 100 98 100 29607 31945 .343 2.919 2.806 3.131 2.943 1.552 80 323 2.933 .96 100 1900 7950 30 40 153 163 0 23316 102 23214 3.073 24894 24792 .325 2.954 1.62 1.563
4 1111 3251 172 108 939 3143 848 2718 182 116 676 2610 0 0 923 2597 61 46 91 100 75 100 4082 3286 .299 3.347 3.861 4.72 4.489 1.99 12 88 3.267 .89 50 2050 7960 33 38 170 175 0 3422 114 3308 3.523 2861 2747 .284 4.064 1.817 2.023
5 3234 14094 175 103 3059 13991 3629 16083 182 127 3454 15980 0 0 1328 5685 57 122 98 100 97 98 17050 19434 .219 4.574 4.627 4.751 4.537 1.581 80 322 4.642 .97 100 2180 7940 29 39 181 191 0 14836 108 14727 4.814 16929 16821 .208 4.87 2.267 2.284
6 328 576 179 106 149 470 191 138 197 172 12 32 0 0 405 1047 100 268 26 26 20 22 619 44 .317 3.154 2.667 1.3 1.905 5.062 80 271 2.906 .91 100 2310 7950 30 40 194 204 -50 606 112 495 3.32 145 34 .301 2.807 1.731 1.489
7 3308 5253 180 107 3128 5146 3607 5317 197 152 3427 5210 0 0 1252 1831 94 237 97 100 97 100 8274 8637 .608 1.645 1.52 1.798 1.695 1.615 80 283 1.627 .96 100 2450 7950 30 40 208 218 0 5529 113 5417 1.732 5597 5484 .577 1.6 .792 .678
8 1575 2526 176 105 1399 2421 1620 2430 187 122 1444 2325 0 0 508 1025 92 123 98 100 97 100 3820 3769 .578 1.731 1.61 1.693 1.672 1.447 80 277 1.836 .93 100 2590 7950 30 40 222 232 0 2659 111 2548 1.822 2558 2447 .549 1.695 .865 .761
9 1658 3506 174 103 1484 3403 1389 2770 179 108 1215 2667 0 0 1152 2501 39 33 100 100 100 100 4887 3882 .436 2.293 2.195 2.438 2.495 1.56 52 181 2.339 .93 80 2740 7960 32 40 238 246 0 3691 108 3582 2.414 2916 2807 .414 2.311 1.271 1.208
10 598 990 177 104 421 886 574 1033 179 107 397 929 0 0 154 331 42 33 100 100 100 100 1307 1326 .475 2.105 2.34 2.085 1.995 1.456 52 247 2.143 .88 90 2860 7940 29 38 249 258 0 1042 109 933 2.215 1087 978 .451 2.463 1.147 1.301
11 5253 31370 174 102 5079 31268 5505 33046 178 107 5331 32944 0 0 1309 6493 42 34 100 100 100 100 36347 38275 .162 6.156 6.18 6.243 6.139 1.241 80 285 6.259 .96 100 3000 7960 31 41 263 273 0 33021 107 32914 6.48 34785 34678 .154 6.505 2.696 2.702
12 1190 3308 178 105 1012 3203 1108 2535 182 109 930 2430 0 0 576 2357 38 32 100 100 100 100 4215 3360 .316 3.165 2.613 2.965 3.115 1.591 52 190 3.852 .89 80 3140 7950 31 39 278 286 0 3482 111 3372 3.332 2668 2558 .3 2.75 1.736 1.46
13 901 5553 181 105 720 5448 875 5373 182 110 694 5268 0 0 325 1572 39 32 100 100 100 100 6168 5962 .132 7.567 7.591 8.23 7.646 1.507 80 268 7.485 .93 100 3270 7950 30 40 290 300 0 5845 111 5735 7.965 5656 5545 .126 7.99 2.994 2.998
14 1588 2389 179 107 1409 2282 1645 2456 177 110 1466 2349 0 0 434 707 40 31 100 100 100 100 3691 3815 .617 1.62 1.602 1.621 1.656 1.363 80 242 1.647 .96 100 3410 7950 30 40 304 314 0 2515 113 2402 1.705 2585 2473 .587 1.687 .77 .754
15 197 203 179 110 18 93 179 120 176 116 0 10 0 0 109 395 40 40 16 27 11 10 111 10 .194 5.167 null 1.54 1.508 3.749 80 238 3.982 .81 100 3530 7950 30 40 316 326 -50 214 116 98 5.439 126 11 .184 null 2.443 null
16 196 120 177 111 19 9 190 116 178 118 13 5 0 0 47 40 39 41 33 17 15 6 28 18 2.111 .474 .385 .646 .571 4.463 80 276 1.419 .14 100 3660 7950 30 40 329 339 -50 126 117 9 .499 122 5 2.006 .405 -1.004 -1.305
17 1793 3102 175 112 1618 2990 1798 3142 188 126 1623 3030 0 0 416 817 73 74 100 100 100 100 4608 4653 .541 1.848 1.867 1.839 1.824 1.243 52 248 1.85 .96 90 3800 7950 30 39 343 352 0 3265 118 3147 1.945 3307 3189 .514 1.965 .96 .975
18 1373 2135 176 112 1197 2023 1443 2162 186 122 1267 2050 0 0 340 606 69 71 98 100 98 100 3220 3317 .592 1.69 1.618 1.67 1.68 1.271 80 282 1.736 .96 100 3940 7950 30 40 357 367 0 2247 118 2129 1.779 2276 2158 .562 1.703 .831 .768
19 875 1124 175 111 700 1013 866 1131 176 112 691 1020 0 0 249 467 39 35 100 100 100 98 1713 1711 .691 1.447 1.476 1.359 1.44 1.587 80 277 1.574 .93 100 4080 7950 30 40 371 381 0 1183 117 1066 1.523 1191 1074 .656 1.554 .607 .636
20 2585 4103 183 117 2402 3986 2636 4386 183 121 2453 4269 0 0 598 1151 40 40 100 100 100 100 6388 6722 .603 1.659 1.74 1.616 1.665 1.354 80 300 1.73 .96 100 4220 7950 30 40 385 395 0 4319 123 4196 1.747 4617 4494 .572 1.832 .805 .873

Total number of rows: 44544

Table truncated, full table size 9791 Kbytes.




Supplementary data files not provided
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