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Sample GSM70926 Query DataSets for GSM70926
Status Public on Aug 20, 2005
Title L1 MTC#1T10 (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#1T10 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#1T10 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13806.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 2891 1813 149 130 2742 1683 2937 1807 158 136 2788 1677 0 0 1115 703 46 46 100 100 100 100 4425 4465 1.629 .614 .602 .617 .61 .119 120 614 .603 .98 130 2010 16610 70 83 50 63 0 1794 129 1665 .607 1788 1660 1.646 .595 -.719 -.748
2 952 1042 144 134 808 908 1007 1029 147 136 863 895 0 0 410 421 36 38 100 100 98 100 1716 1758 .89 1.124 1.037 1.298 1.116 .7 120 500 1.06 .97 120 2150 16580 68 80 65 77 0 1031 133 899 1.112 1018 886 .899 1.026 .153 .037
3 537 353 154 137 383 216 529 345 157 142 375 208 0 0 129 87 37 37 100 100 98 98 599 583 1.773 .564 .555 .599 .544 .26 80 402 .498 .86 100 2320 16570 68 78 83 93 0 349 136 214 .558 341 206 1.792 .549 -.841 -.865
4 2761 2358 168 160 2593 2198 2702 2504 176 169 2534 2344 0 0 926 712 51 60 100 100 100 100 4791 4878 1.18 .848 .925 .87 .842 .153 80 457 .814 .98 110 2490 16590 69 80 99 110 0 2333 158 2175 .839 2478 2320 1.192 .915 -.254 -.128
5 6118 14854 158 137 5960 14717 6231 13034 169 151 6073 12897 0 0 1774 6464 47 59 100 100 100 100 20677 18970 .405 2.469 2.124 2.493 2.238 .838 80 455 2.373 .93 100 2650 16580 69 79 116 126 0 14699 136 14564 2.444 12898 12763 .409 2.102 1.289 1.071
6 1349 810 158 113 1191 697 1528 777 165 116 1370 664 0 0 681 371 40 31 100 100 96 100 1888 2034 1.709 .585 .485 .794 .633 .736 32 216 .536 .94 70 2840 16570 69 76 136 143 0 802 112 690 .579 769 657 1.727 .48 -.788 -1.06
7 2676 1064 161 114 2515 950 2795 1070 185 125 2634 956 0 0 535 214 265 75 100 100 100 100 3465 3590 2.647 .378 .363 .384 .382 .067 80 504 .357 .97 110 2980 16580 68 79 148 159 0 1053 113 940 .374 1059 946 2.675 .359 -1.42 -1.477
8 3301 546 183 140 3118 406 2838 530 247 154 2655 390 0 0 1817 146 403 107 100 100 96 90 3524 3045 7.68 .13 .147 .163 .152 .081 32 217 .094 .83 70 3160 16560 68 75 168 175 0 540 139 402 .129 524 386 7.761 .145 -2.956 -2.782
9 11061 473 183 145 10878 328 11260 482 196 150 11077 337 0 0 1879 101 67 42 100 100 100 98 11206 11414 33.165 .03 .03 .03 .03 .009 80 401 .029 .92 100 3300 16580 69 79 181 191 0 468 143 325 .03 477 333 33.514 .03 -5.067 -5.054
10 1167 613 183 161 984 452 1178 604 204 175 995 443 0 0 228 130 75 65 100 100 100 100 1436 1438 2.177 .459 .445 .465 .459 .112 52 313 .431 .92 90 3450 16570 68 77 196 205 0 607 159 447 .455 598 438 2.2 .441 -1.137 -1.183
11 7503 7436 182 154 7321 7282 7796 7610 200 171 7614 7456 0 0 1607 1574 70 71 100 100 100 100 14603 15070 1.005 .995 .979 1.005 1.005 .142 80 479 .962 .98 110 3610 16570 67 78 211 222 0 7359 152 7206 .984 7531 7378 1.016 .969 -.023 -.045
12 831 877 168 147 663 730 829 890 176 151 661 743 0 0 209 217 44 41 100 100 98 100 1393 1404 .908 1.101 1.124 1.173 1.105 .436 80 394 1.023 .94 100 3780 16570 68 78 229 239 0 868 145 722 1.09 881 735 .918 1.112 .124 .154
13 3801 2956 164 148 3637 2808 3337 2641 170 152 3173 2493 0 0 2415 1712 45 41 98 100 97 100 6445 5666 1.295 .772 .786 1.051 .78 1.246 120 523 .733 .98 120 3940 16570 67 79 244 256 0 2925 146 2779 .764 2613 2467 1.309 .778 -.388 -.363
14 541 331 167 148 374 183 546 327 170 151 379 179 0 0 85 76 38 38 100 96 100 94 557 558 2.044 .489 .472 .495 .477 .2 52 256 .451 .82 80 4090 16570 69 77 261 269 0 328 146 181 .484 324 177 2.065 .467 -1.046 -1.097
15 723 433 167 148 556 285 684 419 174 151 517 271 0 0 225 121 49 35 100 100 98 96 841 788 1.951 .513 .524 .575 .528 .371 80 398 .465 .89 100 4260 16570 68 78 277 287 0 428 146 282 .507 415 268 1.971 .519 -.979 -.947
16 683 455 174 160 509 295 690 443 181 163 516 283 0 0 166 109 54 42 100 100 98 98 804 799 1.725 .58 .548 .634 .562 .346 80 372 .516 .87 100 4420 16570 68 78 293 303 0 450 158 292 .574 438 280 1.744 .543 -.802 -.882
17 10327 16635 174 158 10153 16477 11598 18956 180 163 11424 18798 0 0 3785 6039 52 45 100 100 100 100 26630 30222 .616 1.623 1.645 1.693 1.605 .619 80 450 1.588 .98 110 4570 16570 67 78 307 318 0 16462 156 16305 1.606 18758 18602 .623 1.628 .683 .703
18 527 351 171 149 356 202 516 340 177 153 345 191 0 0 90 77 42 41 100 100 100 94 558 536 1.762 .567 .554 .604 .537 .317 52 344 .479 .81 90 4740 16560 67 76 325 334 0 347 147 200 .562 336 189 1.781 .548 -.833 -.868
19 1785 1640 170 147 1615 1493 1802 1719 180 151 1632 1572 0 0 379 360 80 53 100 100 100 100 3108 3204 1.082 .924 .963 .945 .942 .251 80 471 .889 .96 110 4900 16560 66 77 340 351 0 1623 145 1477 .915 1701 1556 1.093 .953 -.128 -.069
20 3967 991 168 148 3799 843 3999 932 178 154 3831 784 0 0 927 235 80 55 100 100 100 100 4642 4615 4.507 .222 .205 .223 .219 .035 80 458 .215 .97 110 5070 16560 66 77 357 368 0 981 146 834 .22 922 776 4.554 .203 -2.187 -2.304

Total number of rows: 21504

Table truncated, full table size 4876 Kbytes.




Supplementary data files not provided

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