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Sample GSM70922 Query DataSets for GSM70922
Status Public on Aug 20, 2005
Title L1 MTC#1T7 (red, channel 2) vs. RefB-JW (green, channel 1)
Sample type RNA
 
Channel 1
Source name RefB-JW (green)
Organism Caenorhabditis elegans
Characteristics RefB-JW (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name L1 MTC#1T7 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#1T7 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13802.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 18, 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 GPL2653
Series (1)
GSE3169 Global analysis of dauer gene expression in Caenorhabditis elegans

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 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
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

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
1 5246 2649 178 97 5068 2552 5600 2680 183 102 5422 2583 0 0 2234 855 44 29 100 100 100 100 7620 8005 1.986 .504 .476 .589 .489 .25 52 291 .462 .97 90 1440 16600 43 52 55 64 0 2584 95 2489 .491 2614 2520 2.036 .465 -1.026 -1.106
2 2266 1847 172 94 2094 1753 2333 1838 175 96 2161 1744 0 0 646 466 38 27 100 100 100 100 3847 3905 1.195 .837 .807 .907 .818 .321 52 320 .793 .97 80 1610 16580 42 50 73 81 0 1802 92 1710 .817 1793 1701 1.225 .787 -.292 -.345
3 923 611 161 91 762 520 907 607 166 98 746 516 0 0 171 91 38 34 100 100 100 100 1282 1262 1.465 .682 .692 .714 .679 .199 32 236 .6 .92 70 1770 16570 41 48 89 96 0 596 89 507 .666 592 503 1.502 .675 -.587 -.568
4 3460 2967 164 96 3296 2871 3900 3361 172 100 3736 3265 0 0 1502 1093 47 34 100 100 100 100 6167 7001 1.148 .871 .874 1.017 .864 .638 52 376 .804 .98 90 1930 16560 39 48 104 113 0 2894 94 2801 .85 3279 3185 1.177 .852 -.235 -.23
5 7762 4497 194 110 7568 4387 7416 4387 209 117 7222 4277 0 0 3020 1353 82 45 100 100 100 100 11955 11499 1.725 .58 .592 .608 .588 .139 52 318 .514 .97 80 2090 16570 41 49 121 129 0 4387 107 4279 .565 4279 4172 1.768 .578 -.822 -.792
6 1779 991 199 105 1580 886 1220 949 209 107 1021 844 0 0 1501 622 70 36 100 100 100 100 2466 1865 1.783 .561 .827 .763 .533 .537 12 98 .481 .97 50 2280 16550 40 45 141 146 0 967 102 864 .547 926 823 1.828 .806 -.87 -.31
7 3501 1337 161 91 3340 1246 3354 1252 166 94 3193 1161 0 0 883 327 33 26 100 100 100 100 4586 4354 2.681 .373 .364 .384 .363 .097 52 319 .355 .98 80 2430 16560 40 48 155 163 0 1304 89 1215 .364 1221 1133 2.748 .355 -1.458 -1.495
8 1860 1375 160 93 1700 1282 1888 1403 163 94 1728 1310 0 0 462 299 33 25 100 100 100 100 2982 3038 1.326 .754 .758 .781 .784 .175 32 230 .68 .96 70 2590 16550 39 46 171 178 0 1341 91 1251 .736 1369 1278 1.359 .74 -.443 -.435
9 10857 843 172 93 10685 750 11367 844 176 95 11195 751 0 0 2319 213 46 27 100 100 100 100 11435 11946 14.247 .07 .067 .07 .069 .015 52 362 .068 .97 90 2760 16570 40 49 187 196 0 822 91 732 .068 823 733 14.605 .065 -3.868 -3.934
10 1486 1051 167 98 1319 953 1489 1029 170 100 1322 931 0 0 369 267 42 26 100 100 100 100 2272 2253 1.384 .723 .704 .769 .719 .307 52 282 .692 .97 80 2920 16560 40 48 204 212 0 1025 96 930 .705 1004 908 1.419 .687 -.505 -.542
11 9474 7256 168 98 9306 7158 10114 7891 235 119 9946 7793 0 0 3810 2705 1206 202 97 100 93 100 16464 17739 1.3 .769 .784 .839 .773 .394 80 435 .739 .98 100 3070 16550 38 48 218 228 0 7078 96 6982 .75 7697 7602 1.333 .764 -.414 -.388
12 1357 1397 165 93 1192 1304 1286 1400 168 94 1121 1307 0 0 486 434 35 26 100 100 100 100 2496 2428 .914 1.094 1.166 1.227 1.054 .596 52 305 .998 .96 80 3230 16560 40 48 235 243 0 1363 91 1272 1.067 1366 1275 .937 1.137 .094 .186
13 6465 4015 165 95 6300 3920 6836 4025 166 99 6671 3930 0 0 2232 1136 33 32 100 100 100 100 10220 10601 1.607 .622 .589 .675 .63 .255 32 230 .599 .98 70 3400 16540 38 45 252 259 0 3917 93 3824 .607 3926 3834 1.648 .575 -.72 -.799
14 1331 1115 166 96 1165 1019 1334 1109 184 117 1168 1013 0 0 364 252 172 194 98 100 96 96 2184 2181 1.143 .875 .867 1.112 .906 1.531 52 366 .83 .96 90 3560 16550 38 47 267 276 0 1088 94 994 .853 1082 988 1.172 .846 -.229 -.241
15 3253 2348 167 94 3086 2254 3262 2347 181 109 3095 2253 0 0 976 553 166 187 100 100 98 100 5340 5348 1.369 .73 .728 .815 .76 .456 52 355 .691 .96 90 3720 16550 38 47 283 292 0 2290 92 2199 .712 2289 2198 1.404 .71 -.489 -.494
16 1864 1796 166 97 1698 1699 1925 1844 174 107 1759 1747 0 0 393 333 58 88 100 100 100 100 3397 3506 .999 1.001 .993 1.031 .985 .207 52 364 .943 .97 90 3880 16550 38 47 299 308 0 1752 95 1657 .976 1799 1704 1.025 .969 -.035 -.046
17 11321 17078 167 94 11154 16984 13077 20453 171 98 12910 20359 0 0 5377 7539 32 30 100 100 100 100 28138 33269 .657 1.523 1.577 1.674 1.522 .562 80 439 1.471 .99 100 4050 16550 38 48 316 326 0 16659 92 16568 1.485 19951 19860 .673 1.538 .571 .621
18 1490 1284 166 95 1324 1189 1518 1358 168 100 1352 1263 0 0 313 294 30 32 100 100 100 100 2513 2615 1.114 .898 .934 .91 .897 .207 52 300 .864 .97 80 4220 16540 38 46 334 342 0 1253 93 1160 .876 1325 1232 1.142 .911 -.191 -.134
19 3337 2806 167 94 3170 2712 3392 2875 168 98 3225 2781 0 0 811 493 30 31 100 100 100 100 5882 6006 1.169 .856 .862 .897 .846 .216 52 333 .802 .97 90 4380 16550 38 47 349 358 0 2737 92 2645 .835 2804 2713 1.198 .841 -.261 -.25
20 3792 1187 166 94 3626 1093 4022 1320 167 96 3856 1226 0 0 1173 422 30 26 100 100 100 100 4719 5082 3.317 .301 .318 .297 .309 .076 80 431 .298 .97 100 4530 16540 37 47 364 374 0 1158 92 1066 .294 1288 1196 3.401 .31 -1.766 -1.689

Total number of rows: 21504

Table truncated, full table size 4811 Kbytes.




Supplementary data files not provided
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