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Sample GSM93995 Query DataSets for GSM93995
Status Public on Jan 28, 2006
Title 2.1a vs 2.1b
Sample type RNA
 
Channel 1
Source name fluoranthen
Organism Caenorhabditis elegans
Characteristics fluoranthen
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name control
Organism Caenorhabditis elegans
Characteristics control
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33669.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 GPL3396
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
1 231 127 206 115 25 12 222 118 218 122 16 3 0 0 95 46 82 38 38 17 5 1 37 19 2.083 .48 .188 1 1 1 52 335 1 .04 90 1590 18900 32 41 82 91 -50 163 147 15 .615 151 4 1.625 .24 -.7 -2.057
2 4787 1631 215 130 4572 1501 4985 1824 226 140 4770 1694 0 0 2366 640 83 53 100 100 100 96 6073 6464 3.046 .328 .355 1 1 1 32 148 1 .93 60 1700 18920 36 42 95 101 0 2091 167 1924 .421 2338 2172 2.376 .455 -1.248 -1.135
3 2028 558 220 138 1808 420 2019 564 234 143 1799 426 0 0 589 115 97 42 100 100 100 100 2228 2225 4.305 .232 .237 1 1 1 52 294 1 .93 80 1870 18910 34 42 111 119 0 715 177 538 .298 723 546 3.358 .304 -1.747 -1.72
4 1500 223 224 121 1276 102 1553 217 246 127 1329 96 0 0 251 50 126 37 100 92 100 65 1378 1425 12.51 .08 .072 1 1 1 52 338 1 .74 90 2010 18910 33 42 124 133 0 286 155 131 .102 278 123 9.758 .093 -3.287 -3.433
5 2744 3571 228 112 2516 3459 3158 4087 245 116 2930 3975 0 0 1250 1970 109 31 94 98 92 98 5975 6905 .727 1.375 1.357 1 1 1 52 305 1 .9 80 2180 18920 35 43 142 150 0 4578 144 4435 1.763 5240 5096 .567 1.739 .818 .799
6 2720 1551 231 113 2489 1438 2781 1624 253 121 2550 1511 0 0 573 387 308 69 100 100 100 100 3927 4061 1.731 .578 .593 1 1 1 52 311 1 .93 80 2350 18920 35 43 159 167 0 1988 145 1844 .741 2082 1937 1.35 .76 -.433 -.397
7 2108 2135 235 116 1873 2019 2193 2068 269 126 1958 1952 0 0 763 1084 356 79 96 100 87 100 3892 3910 .928 1.078 .997 1 1 1 32 230 1 .94 70 2500 18920 35 42 174 181 0 2737 149 2588 1.382 2651 2503 .724 1.278 .467 .354
8 5118 3672 212 116 4906 3556 5790 4255 230 122 5578 4139 0 0 2236 1466 94 32 100 100 100 100 8462 9717 1.38 .725 .742 1 1 1 52 312 1 .97 80 2660 18920 35 43 190 198 0 4708 149 4559 .929 5455 5306 1.076 .951 -.106 -.072
9 1363 674 222 117 1141 557 1394 755 237 122 1172 638 0 0 341 268 90 32 100 100 100 96 1698 1810 2.048 .488 .544 1 1 1 32 176 1 .88 60 2820 18910 35 41 207 213 0 864 150 714 .626 968 818 1.598 .698 -.676 -.519
10 1372 5448 246 130 1126 5318 284 179 952 3449 38 49 0 0 2191 10189 1949 8930 21 23 15 13 6444 87 .212 4.723 1.289 1 1 1 52 319 1 .96 90 3040 18900 32 41 227 236 -50 6985 167 6818 6.055 229 63 .165 1.653 2.598 .725
11 1646 1310 221 117 1425 1193 1687 1366 234 119 1466 1249 0 0 431 301 84 31 100 100 100 100 2618 2715 1.194 .837 .852 1 1 1 52 234 1 .92 80 3140 18920 35 43 238 246 0 1679 150 1529 1.073 1751 1601 .932 1.092 .102 .127
12 9173 11629 224 120 8949 11509 9336 11480 235 136 9112 11360 0 0 2134 2048 93 145 100 100 100 100 20458 20472 .778 1.286 1.247 1 1 1 52 295 1 .97 80 3300 18920 35 43 254 262 0 14909 154 14755 1.649 14718 14564 .607 1.598 .721 .677
13 2645 2940 231 128 2414 2812 2606 2660 272 169 2375 2532 0 0 1089 1798 239 248 100 100 100 92 5226 4907 .858 1.165 1.066 1 1 1 52 360 1 .92 90 3460 18920 34 43 269 278 0 3769 164 3605 1.493 3410 3246 .67 1.367 .579 .451
14 2588 6819 222 120 2366 6699 2575 6963 236 124 2353 6843 0 0 536 1475 92 38 100 100 100 100 9065 9196 .353 2.831 2.908 1 1 1 52 385 1 .95 90 3690 18910 33 42 292 301 0 8742 154 8588 3.63 8927 8773 .275 3.728 1.86 1.899
15 3254 11767 217 113 3037 11654 3227 11902 233 120 3010 11789 0 0 1128 3632 103 36 100 100 100 100 14691 14799 .261 3.837 3.917 1 1 1 52 288 1 .95 80 3860 18920 35 43 310 318 0 15086 145 14941 4.92 15259 15114 .203 5.021 2.299 2.328
16 1203 677 209 112 994 565 1183 699 220 116 974 587 0 0 355 164 87 32 100 100 100 100 1559 1561 1.759 .568 .603 1 1 1 52 312 1 .9 90 4020 18920 34 43 325 334 0 868 144 724 .729 896 753 1.372 .773 -.457 -.372
17 1711 1931 217 112 1494 1819 1686 2097 232 132 1469 1985 0 0 539 565 115 110 100 100 100 100 3313 3454 .821 1.218 1.351 1 1 1 52 373 1 .93 90 4160 18910 33 42 339 348 0 2476 144 2332 1.561 2688 2545 .641 1.732 .642 .793
18 2052 3063 202 114 1850 2949 2128 3059 217 123 1926 2945 0 0 825 980 91 41 100 100 100 100 4799 4871 .627 1.594 1.529 1 1 1 32 230 1 .94 70 4340 18910 34 41 358 365 0 3927 146 3781 2.044 3922 3776 .489 1.96 1.031 .971
19 934 177 200 111 734 66 945 177 213 116 745 66 0 0 189 40 86 33 100 82 100 50 800 811 11.121 .09 .089 1 1 1 52 312 1 .62 80 4490 18910 34 42 373 381 0 227 142 85 .115 227 85 8.675 .114 -3.117 -3.138
20 853 308 206 118 647 190 867 320 227 124 661 202 0 0 220 116 99 36 96 90 96 78 837 863 3.405 .294 .306 1 1 1 32 230 1 .75 70 4640 18910 34 41 388 395 0 395 151 244 .376 410 259 2.656 .392 -1.409 -1.352

Total number of rows: 21888

Table truncated, full table size 4682 Kbytes.




Supplementary data files not provided
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