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Sample GSM70983 Query DataSets for GSM70983
Status Public on Aug 20, 2005
Title Dauer MTC#4T3-2 (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 Dauer MTC#4T3-2 (red)
Organism Caenorhabditis elegans
Characteristics Dauer MTC#4T3-2 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11503.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 GPL2655
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 2440 1435 161 142 2279 1293 null null 169 157 null null null null null null null null 100 100 null null null null 1.763 .567 null null 1.786 null 52 281 .543 .97 null null null 33 42 66 75 0 1148 113 1035 .454 null null 2.202 null -1.139 null
2 891 1589 164 135 727 1454 null null 177 166 null null null null null null null null 100 100 null null null null .5 2 null null .472 null 52 392 1.687 .92 null null null 33 42 85 94 0 1271 108 1163 1.6 null null .625 null .678 null
3 411 304 164 134 247 170 null null 174 157 null null null null null null null null 100 81 null null null null 1.453 .688 null null 1.335 null 32 225 .537 .79 null null null 33 40 101 108 0 243 107 136 .551 null null 1.816 null -.861 null
4 1920 2202 163 132 1757 2070 null null 172 138 null null null null null null null null 100 100 null null null null .849 1.178 null null .851 null 52 309 1.163 .97 null null null 34 42 118 126 0 1761 105 1656 .943 null null 1.061 null -.085 null
5 5230 2062 170 129 5060 1933 null null 175 132 null null null null null null null null 100 100 null null null null 2.618 .382 null null 2.615 null 52 316 .383 .97 null null null 34 42 134 142 0 1649 103 1546 .306 null null 3.273 null -1.711 null
6 445 378 155 127 290 251 null null 157 129 null null null null null null null null 84 78 null null null null 1.155 .866 null null 1.185 null 32 225 .775 .89 null null null 33 40 151 158 0 302 101 201 .693 null null 1.443 null -.529 null
7 1688 1288 157 127 1531 1161 null null 159 130 null null null null null null null null 100 100 null null null null 1.319 .758 null null 1.319 null 80 469 .729 .96 null null null 33 43 166 176 0 1030 101 929 .607 null null 1.648 null -.721 null
8 594 601 158 127 436 474 null null 163 133 null null null null null null null null 100 100 null null null null .92 1.087 null null .969 null 32 230 .934 .91 null null null 34 41 183 190 0 480 101 379 .869 null null 1.15 null -.202 null
9 6339 3043 164 137 6175 2906 null null 186 159 null null null null null null null null 100 100 null null null null 2.125 .471 null null 2.089 null 52 385 .448 .98 null null null 33 42 198 207 0 2434 109 2325 .377 null null 2.656 null -1.409 null
10 810 1684 165 135 645 1549 null null 286 155 null null null null null null null null 0 100 null null null null .416 2.402 null null .43 null 52 344 .121 .19 null null null 34 43 215 224 0 1347 108 1239 1.921 null null .521 null .942 null
11 7882 12706 174 141 7708 12565 null null 313 153 null null null null null null null null 100 100 null null null null .613 1.63 null null .604 null 80 507 1.331 .88 null null null 32 43 230 241 0 10164 112 10052 1.304 null null .767 null .383 null
12 698 528 175 151 523 377 null null 199 166 null null null null null null null null 100 100 null null null null 1.387 .721 null null 1.434 null 32 224 .125 .4 null null null 34 41 248 255 0 422 120 302 .577 null null 1.732 null -.792 null
13 4904 6711 160 134 4744 6577 null null 176 151 null null null null null null null null 100 100 null null null null .721 1.386 null null .726 null 32 236 1.333 .96 null null null 35 42 265 272 0 5368 107 5261 1.109 null null .902 null .149 null
14 562 472 158 129 404 343 null null 160 130 null null null null null null null null 100 100 null null null null 1.178 .849 null null 1.134 null 32 236 .733 .87 null null null 35 42 280 287 0 377 103 274 .678 null null 1.474 null -.56 null
15 966 1061 155 129 811 932 null null 157 130 null null null null null null null null 98 100 null null null null .87 1.149 null null .805 null 52 321 1.008 .93 null null null 35 43 296 304 0 848 103 745 .919 null null 1.089 null -.122 null
16 945 1052 153 135 792 917 null null 156 138 null null null null null null null null 100 100 null null null null .864 1.158 null null .934 null 32 236 1.028 .9 null null null 35 42 312 319 0 841 108 733 .926 null null 1.08 null -.112 null
17 11000 21161 155 135 10845 21026 null null 171 193 null null null null null null null null 100 100 null null null null .516 1.939 null null .499 null 32 236 1.882 .98 null null null 35 42 327 334 0 16928 108 16820 1.551 null null .645 null .633 null
18 766 996 157 139 609 857 null null 172 161 null null null null null null null null 100 100 null null null null .711 1.407 null null .702 null 32 236 1.188 .89 null null null 36 43 344 351 0 796 111 685 1.125 null null .889 null .17 null
19 2540 3403 167 152 2373 3251 null null 192 182 null null null null null null null null 100 100 null null null null .73 1.37 null null .742 null 52 302 1.272 .97 null null null 35 43 361 369 0 2722 121 2601 1.096 null null .912 null .132 null
20 6105 1862 165 144 5940 1718 null null 187 168 null null null null null null null null 100 100 null null null null 3.458 .289 null null 3.472 null 80 431 .283 .97 null null null 34 44 376 386 0 1489 115 1374 .231 null null 4.323 null -2.112 null

Total number of rows: 21504

Table truncated, full table size 5177 Kbytes.




Supplementary data files not provided
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