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Sample GSM85967 Query DataSets for GSM85967
Status Public on Dec 03, 2005
Title 6HR-7
Sample type RNA
 
Channel 1
Source name 18T (EtOH-treated) (green, channel 1)
Organism Caenorhabditis elegans
Characteristics 18T (EtOH-treated) (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 18C (N2) (red, channel 2)
Organism Caenorhabditis elegans
Characteristics 18C (N2) (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12240.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 Dec 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 GPL2646
Series (1)
GSE3727 Ethanol-response genes and their regulation

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 18434 13155 2220 1400 16214 11755 null null 2001 1274 null null null null null null null null 90 95 null null null null 1.379 .725 null null 1.378 null 80 470 .683 .96 null null null 105 116 65 76 0 12649 1346 11303 .697 null null 1.434 null -.521 null
2 16067 6931 2007 1293 14060 5638 null null 2028 1302 null null null null null null null null 86 88 null null null null 2.494 .401 null null 2.329 null 120 474 .391 .95 null null null 105 117 82 94 0 6664 1243 5421 .386 null null 2.594 null -1.375 null
3 5498 3986 1886 1226 3612 2760 null null 1907 1226 null null null null null null null null 88 92 null null null null 1.309 .764 null null 1.36 null 80 405 .698 .94 null null null 105 116 98 109 0 3832 1178 2654 .735 null null 1.361 null -.445 null
4 10193 7932 1825 1156 8368 6776 null null 1835 1166 null null null null null null null null 96 98 null null null null 1.235 .81 null null 1.277 null 80 442 .757 .95 null null null 106 117 114 125 0 7626 1111 6515 .779 null null 1.284 null -.361 null
5 6819 18160 1691 1079 5128 17081 null null 1705 1089 null null null null null null null null 90 100 null null null null .3 3.331 null null .299 null 80 452 3.087 .95 null null null 106 117 131 142 0 17461 1037 16424 3.203 null null .312 null 1.679 null
6 3246 2292 1582 1002 1664 1290 null null 1585 1017 null null null null null null null null 75 92 null null null null 1.29 .775 null null 1.276 null 52 270 .635 .88 null null null 106 114 149 157 0 2203 963 1240 .745 null null 1.342 null -.424 null
7 11206 9057 1482 950 9724 8107 null null 1484 958 null null null null null null null null 91 95 null null null null 1.199 .834 null null 1.193 null 120 547 .806 .97 null null null 104 117 162 175 0 8708 913 7795 .802 null null 1.247 null -.319 null
8 4348 3070 1387 909 2961 2161 null null 1402 915 null null null null null null null null 79 85 null null null null 1.37 .73 null null 1.382 null 120 484 .699 .96 null null null 104 117 179 192 0 2951 874 2077 .701 null null 1.426 null -.512 null
9 34024 18935 1337 876 32687 18059 null null 1351 881 null null null null null null null null 94 100 null null null null 1.81 .552 null null 1.793 null 120 477 .53 .97 null null null 104 117 195 208 0 18206 842 17364 .531 null null 1.882 null -.913 null
10 5580 5699 1356 864 4224 4835 null null 1365 868 null null null null null null null null 85 93 null null null null .874 1.145 null null .902 null 120 407 1.092 .97 null null null 106 118 211 223 0 5479 830 4649 1.101 null null .909 null .138 null
11 4200 3477 1321 828 2879 2649 null null 1321 834 null null null null null null null null 84 93 null null null null 1.087 .92 null null 1.144 null 120 464 .865 .96 null null null 104 116 227 239 0 3343 796 2547 .885 null null 1.13 null -.177 null
12 3704 3188 1258 774 2446 2414 null null 1259 787 null null null null null null null null 78 94 null null null null 1.013 .987 null null 1.014 null 120 487 .89 .95 null null null 105 117 243 255 0 3065 744 2321 .949 null null 1.054 null -.076 null
13 8735 7581 1145 730 7590 6851 null null 1157 727 null null null null null null null null 93 96 null null null null 1.108 .903 null null 1.158 null 80 412 .836 .96 null null null 105 116 260 271 0 7289 701 6588 .868 null null 1.152 null -.204 null
14 3372 2353 1109 691 2263 1662 null null 1115 689 null null null null null null null null 88 93 null null null null 1.362 .734 null null 1.386 null 80 384 .68 .95 null null null 106 116 277 287 0 2262 664 1598 .706 null null 1.416 null -.502 null
15 3052 2503 1071 668 1981 1835 null null 1029 634 null null null null null null null null 83 95 null null null null 1.08 .926 null null 1.066 null 80 387 .848 .95 null null null 106 116 293 303 0 2406 642 1764 .89 null null 1.123 null -.167 null
16 3939 3076 1071 669 2868 2407 null null 987 626 null null null null null null null null 87 95 null null null null 1.192 .839 null null 1.203 null 80 447 .787 .96 null null null 105 116 308 319 0 2957 643 2314 .807 null null 1.239 null -.31 null
17 19492 10684 1106 696 18386 9988 null null 1085 694 null null null null null null null null 92 100 null null null null 1.841 .543 null null 1.865 null 80 412 .521 .98 null null null 105 116 324 335 0 10273 669 9604 .522 null null 1.914 null -.937 null
18 3114 2411 1106 692 2008 1719 null null 1111 699 null null null null null null null null 80 80 null null null null 1.168 .856 null null 1.147 null 120 458 .81 .97 null null null 105 117 341 353 0 2318 665 1653 .823 null null 1.215 null -.281 null
19 5490 5442 1074 694 4416 4748 null null 1084 698 null null null null null null null null 94 100 null null null null .93 1.075 null null .942 null 120 508 1.019 .97 null null null 103 116 355 368 0 5232 667 4565 1.034 null null .967 null .048 null
20 20724 12669 1059 699 19665 11970 null null 1070 701 null null null null null null null null 98 97 null null null null 1.643 .609 null null 1.634 null 120 527 .587 .97 null null null 104 117 371 384 0 12181 672 11509 .585 null null 1.709 null -.773 null

Total number of rows: 21504

Table truncated, full table size 5293 Kbytes.




Supplementary data files not provided
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