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Sample GSM93996 Query DataSets for GSM93996
Status Public on Jan 28, 2006
Title 10a (control) (red, channel 2) vs. 10b (clofibrate) (green, channel 1)
Sample type RNA
 
Channel 1
Source name 10b (clofibrate) (green, channel 1)
Organism Caenorhabditis elegans
Characteristics 10b (clofibrate) (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 10a (control) (red, channel 2)
Organism Caenorhabditis elegans
Characteristics 10a (control) (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14317.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 Jan 27, 2006
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 GPL2655
Series (1)
GSE4111 Expression profiling of five different xenobiotics using a C. elegans microarray

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 3523 1142 59 71 3464 1071 1626 631 64 74 1567 560 0 0 3507 1083 24 24 85 77 80 73 4535 2127 3.234 .309 .357 .727 .329 1.275 120 541 .293 .95 120 1590 18720 54 66 37 49 0 1418 88 1330 .384 784 695 2.605 .444 -1.381 -1.172
2 491 549 64 75 427 474 538 591 72 77 474 516 0 0 217 237 34 23 91 95 91 93 901 990 .901 1.11 1.089 2.002 1.149 5.362 80 346 1.01 .92 110 1760 18720 54 65 54 65 0 682 93 589 1.378 734 641 .725 1.352 .463 .435
3 116 133 66 77 50 56 107 112 97 87 41 35 0 0 57 70 319 71 0 35 0 12 106 76 .893 1.12 .854 1.781 1.028 2.487 120 397 .63 .58 120 1920 18720 54 66 70 82 0 165 96 70 1.391 139 43 .719 1.06 .476 .084
4 1117 775 64 79 1053 696 787 624 70 82 723 545 0 0 1018 651 28 25 76 76 70 73 1749 1268 1.513 .661 .754 1.155 .684 1.587 120 405 .62 .95 120 2080 18720 54 66 86 98 0 962 98 864 .821 775 677 1.218 .936 -.285 -.095
5 1615 1421 66 83 1549 1338 1162 1110 79 86 1096 1027 0 0 2110 1221 93 27 75 88 64 82 2887 2123 1.158 .864 .937 1.411 .963 1.411 120 475 .455 .68 130 2250 18710 52 65 102 115 0 1765 103 1661 1.073 1378 1275 .932 1.164 .101 .219
6 180 172 74 92 106 80 122 125 87 94 48 33 0 0 160 123 91 28 30 55 18 40 186 81 1.325 .755 .688 1.983 .846 4.783 120 524 .364 .66 130 2400 18700 51 64 117 130 0 214 114 99 .937 155 41 1.067 .854 -.094 -.228
7 918 551 76 95 842 456 1119 591 86 97 1043 496 0 0 697 363 83 27 72 83 65 77 1298 1539 1.846 .542 .476 1.13 .572 2.311 120 485 .502 .95 130 2570 18720 53 66 134 147 0 684 118 566 .672 734 616 1.487 .591 -.572 -.76
8 299 211 77 99 222 112 238 169 93 100 161 70 0 0 207 128 121 29 59 71 38 53 334 231 1.982 .505 .435 .603 .572 .493 120 348 .408 .78 120 2720 18710 53 65 150 162 0 262 123 139 .626 210 87 1.596 .54 -.675 -.889
9 2587 4759 71 103 2516 4656 2031 3235 86 107 1960 3132 0 0 2314 4419 125 33 74 93 71 87 7172 5092 .54 1.851 1.598 2.876 1.864 3.645 208 557 1.781 .98 160 2880 18720 52 68 164 180 0 5910 128 5782 2.298 4017 3889 .435 1.984 1.2 .989
10 504 720 73 118 431 602 356 423 143 246 283 305 0 0 654 1365 503 1083 28 7 3 3 1033 588 .716 1.397 1.078 1.776 1.337 2.58 256 952 .808 .8 180 3020 18690 48 66 177 195 0 894 147 748 1.734 525 379 .577 1.338 .794 .42
11 3213 1852 105 170 3108 1682 1962 1360 234 455 1857 1190 0 0 3019 1581 748 1671 55 47 51 27 4790 3047 1.848 .541 .641 1.626 .56 3.99 120 389 .512 .97 120 3220 18710 53 65 200 212 0 2300 211 2089 .672 1689 1478 1.488 .796 -.573 -.33
12 279 310 128 168 151 142 269 319 137 174 141 151 0 0 94 93 61 68 88 80 63 56 293 292 1.063 .94 1.071 1.209 .973 .818 80 351 .678 .64 100 3360 18690 52 62 215 225 0 385 209 176 1.168 396 188 .856 1.33 .224 .411
13 1925 1294 111 152 1814 1142 2331 1213 122 157 2220 1061 0 0 1411 871 46 41 91 93 86 92 2956 3281 1.588 .63 .478 .968 .633 1.299 80 459 .598 .96 110 3540 18710 53 64 232 243 0 1607 189 1418 .782 1506 1318 1.279 .593 -.355 -.753
14 170 203 104 158 66 45 170 204 111 158 66 46 0 0 47 48 56 35 57 61 19 30 111 112 1.467 .682 .697 1.066 .697 1.178 52 265 .218 .26 80 3690 18710 55 63 249 257 0 252 196 56 .847 253 57 1.181 .865 -.24 -.208
15 180 201 97 157 83 44 186 197 105 157 89 40 0 0 74 55 46 34 71 52 46 25 127 129 1.886 .53 .449 1.006 .53 1.745 80 417 .36 .45 110 3850 18710 53 64 263 274 0 250 195 55 .658 245 50 1.519 .558 -.603 -.841
16 188 242 93 146 95 96 180 228 101 152 87 82 0 0 86 84 42 34 66 70 50 52 191 169 .99 1.011 .943 2.376 .855 8.509 120 403 .734 .72 120 4010 18720 54 66 279 291 0 301 181 119 1.255 283 102 .797 1.17 .327 .227
17 2703 2143 102 156 2601 1987 2579 2255 124 163 2477 2099 0 0 2321 1752 231 52 66 80 65 76 4588 4576 1.309 .764 .847 1.467 .784 2.304 120 473 .732 .96 130 4170 18720 53 66 294 307 0 2661 194 2467 .949 2800 2606 1.054 1.052 -.076 .073
18 191 226 117 170 74 56 189 218 141 175 72 48 0 0 60 75 256 53 1 45 0 21 130 120 1.321 .757 .667 1.717 .911 5.088 80 382 .144 .59 110 4330 18720 54 65 311 322 0 281 211 70 .94 271 60 1.064 .828 -.09 -.273
19 654 469 114 170 540 299 409 378 120 170 295 208 0 0 531 327 42 38 73 67 63 60 839 503 1.806 .554 .705 1.861 .58 6.863 120 436 .553 .92 120 4490 18720 54 66 327 339 0 582 211 371 .688 469 258 1.454 .876 -.54 -.192
20 712 1235 105 159 607 1076 850 1423 113 161 745 1264 0 0 494 873 40 40 75 82 70 80 1683 2009 .564 1.773 1.697 2.756 1.853 3.375 120 448 1.689 .94 120 4650 18710 53 65 343 355 0 1534 197 1336 2.201 1767 1570 .454 2.107 1.138 1.075

Total number of rows: 21504

Table truncated, full table size 4643 Kbytes.




Supplementary data files not provided
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