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Sample GSM70978 Query DataSets for GSM70978
Status Public on Aug 20, 2005
Title L1 MTC#3T6 (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#3T6 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#3T6 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13827.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 GPL2754
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 4860 2874 210 385 4650 2489 4253 1955 261 408 4043 1570 0 0 2832 2105 319 190 98 97 97 92 7139 5613 1.868 .535 .388 .473 .476 .217 80 457 .585 .96 100 2190 18680 47 57 46 56 0 3420 458 2962 .637 2327 1869 1.57 .462 -.651 -1.114
2 1981 4730 224 376 1757 4354 1960 4516 250 388 1736 4140 0 0 566 1910 126 134 100 100 100 100 6111 5876 .404 2.478 2.385 2.492 2.496 .972 80 425 2.339 .9 100 2340 18690 48 58 61 71 0 5629 447 5182 2.949 5375 4927 .339 2.838 1.56 1.505
3 727 955 295 401 432 554 685 865 296 415 390 464 0 0 273 385 86 132 100 96 100 84 986 854 .78 1.282 1.19 1.312 1.111 .592 32 170 1.027 .77 60 2500 18670 48 54 79 85 0 1137 477 659 1.526 1029 552 .655 1.416 .61 .502
4 262 397 252 384 10 13 254 384 258 393 2 0 0 0 63 79 77 128 18 9 0 0 23 2 .769 1.3 null 2.274 1.034 2.98 32 232 .126 .08 70 2640 18680 48 55 92 99 -50 472 457 15 1.547 457 0 .646 null .63 null
5 8344 3002 283 403 8061 2599 8954 3425 302 420 8671 3022 0 0 3204 1699 117 131 100 98 100 96 10660 11693 3.102 .322 .349 .292 .312 .126 52 400 .341 .94 90 2820 18690 48 57 109 118 0 3573 480 3093 .384 4076 3597 2.606 .415 -1.382 -1.27
6 2111 1727 337 436 1774 1291 2140 1633 340 448 1803 1197 0 0 939 709 155 137 100 100 100 91 3065 3000 1.374 .728 .664 .769 .731 .353 12 68 .656 .9 40 3000 18680 50 54 130 134 0 2055 519 1536 .866 1944 1425 1.155 .79 -.207 -.34
7 5229 2545 260 411 4969 2134 5620 2663 276 419 5360 2252 0 0 1400 989 111 124 100 98 100 98 7103 7612 2.328 .429 .42 .417 .432 .142 80 475 .443 .95 100 3140 18690 48 58 141 151 0 3029 489 2540 .511 3169 2680 1.956 .5 -.968 -1
8 1991 1626 289 417 1702 1209 2010 1509 309 440 1721 1092 0 0 640 461 112 168 100 100 100 100 2911 2813 1.408 .71 .635 .772 .727 .308 32 221 .659 .91 70 3320 18680 48 55 160 167 0 1935 496 1439 .845 1796 1300 1.183 .755 -.242 -.405
9 12405 1045 204 377 12201 668 13262 967 220 394 13058 590 0 0 4844 430 84 122 100 91 98 81 12869 13648 18.265 .055 .045 .053 .05 .025 80 428 .057 .88 100 3470 18680 47 57 174 184 0 1244 449 795 .065 1151 702 15.347 .054 -3.94 -4.217
10 1668 1631 185 365 1483 1266 1657 1588 202 382 1472 1223 0 0 287 433 96 117 100 100 100 100 2749 2695 1.171 .854 .831 .851 .856 .241 52 333 .816 .92 90 3620 18670 46 55 189 198 0 1941 434 1507 1.016 1890 1456 .984 .989 .023 -.016
11 5335 2562 192 371 5143 2191 6188 2450 211 385 5996 2079 0 0 2051 1237 100 113 100 98 98 98 7334 8075 2.347 .426 .347 .46 .417 .443 80 428 .436 .94 100 3790 18670 46 56 206 216 0 3049 442 2608 .507 2916 2474 1.972 .413 -.98 -1.277
12 1161 2072 211 399 950 1673 1172 2005 236 406 961 1606 0 0 208 526 113 126 100 100 100 100 2623 2567 .568 1.761 1.671 1.788 1.705 .551 52 327 1.618 .9 90 3940 18680 47 56 221 230 0 2466 475 1991 2.096 2386 1911 .477 1.989 1.068 .992
13 249 411 195 400 54 11 228 422 309 445 33 22 0 0 90 115 405 215 0 6 0 0 65 55 4.909 .204 .667 5.834 1.422 8.849 32 224 .345 .6 70 4080 18670 47 54 236 243 -50 489 476 13 .242 502 26 4.125 .793 -2.044 -.334
14 557 689 178 379 379 310 564 690 245 406 386 311 0 0 168 229 326 180 61 71 5 40 689 697 1.223 .818 .806 .871 .892 .429 52 347 .539 .72 90 4250 18680 47 56 252 261 0 820 451 369 .973 821 370 1.027 .959 -.039 -.061
15 782 752 176 392 606 360 798 732 238 422 622 340 0 0 177 258 377 202 90 71 9 43 966 962 1.683 .594 .547 .653 .531 .38 32 176 .564 .69 60 4440 18670 48 54 273 279 0 895 467 428 .707 871 405 1.414 .651 -.5 -.62
16 798 961 215 399 583 562 799 918 243 407 584 519 0 0 186 248 109 118 100 96 93 96 1145 1103 1.037 .964 .889 1.074 .966 .593 32 228 .767 .78 70 4580 18680 48 55 286 293 0 1144 475 669 1.147 1093 618 .872 1.058 .198 .081
17 4821 8656 198 398 4623 8258 5511 9675 224 395 5313 9277 0 0 2591 5044 90 118 100 100 100 100 12881 14590 .56 1.786 1.746 1.794 1.686 .877 52 381 1.733 .97 90 4760 18660 45 54 303 312 0 10302 474 9828 2.126 11515 11041 .47 2.078 1.088 1.055
18 673 889 166 389 507 500 637 871 192 394 471 482 0 0 152 283 129 124 100 93 96 84 1007 953 1.014 .986 1.023 1.055 .964 .604 32 170 .906 .73 60 4920 18660 47 53 321 327 0 1058 463 595 1.174 1037 574 .852 1.218 .231 .284
19 1783 1690 181 389 1602 1301 1858 1667 207 396 1677 1278 0 0 539 561 118 119 100 98 100 96 2903 2955 1.231 .812 .762 .817 .802 .274 52 346 .753 .91 90 5070 18660 45 54 334 343 0 2011 463 1548 .967 1984 1521 1.035 .907 -.049 -.141
20 2705 1178 204 383 2501 795 2870 1236 213 394 2666 853 0 0 813 459 73 114 100 95 100 87 3296 3519 3.146 .318 .32 .3 .308 .121 80 456 .323 .9 100 5220 18680 47 57 349 359 0 1402 456 946 .378 1471 1015 2.643 .381 -1.402 -1.393

Total number of rows: 21504

Table truncated, full table size 4811 Kbytes.




Supplementary data files not provided
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