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Sample GSM70929 Query DataSets for GSM70929
Status Public on Aug 20, 2005
Title L1 MTC#1T12 (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#1T12 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#1T12 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13809.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 4710 4936 81 103 4629 4833 4607 4745 85 109 4526 4642 0 0 2436 2422 26 34 98 99 98 99 9462 9168 .958 1.044 1.026 1.525 1.035 3.559 156 785 1.01 .98 140 2260 16240 49 63 79 93 0 4440 93 4347 .939 4268 4176 1.065 .923 -.091 -.116
2 1249 1837 78 98 1171 1739 1330 1900 81 101 1252 1802 0 0 471 587 19 29 98 99 96 99 2910 3054 .673 1.485 1.439 2.117 1.484 3.667 120 459 1.387 .97 120 2430 16240 50 62 97 109 0 1652 88 1564 1.336 1709 1621 .749 1.295 .418 .373
3 480 536 78 104 402 432 490 558 82 106 412 454 0 0 141 153 21 30 100 100 100 100 834 866 .931 1.075 1.102 1.163 1.097 .585 80 318 1.014 .94 100 2590 16230 50 60 114 124 0 482 94 389 .967 502 408 1.034 .991 -.049 -.013
4 3356 2915 82 120 3274 2795 3195 2980 87 134 3113 2860 0 0 1656 1290 28 67 100 100 100 99 6069 5973 1.171 .854 .919 1.02 .848 1.144 120 487 .811 .98 120 2750 16240 50 62 129 141 0 2622 108 2514 .768 2681 2573 1.302 .826 -.381 -.275
5 6286 43629 85 122 6201 43507 6463 38769 90 137 6378 38647 0 21 1936 16328 34 70 100 100 100 100 49708 45025 .143 7.016 6.059 7.046 7.105 1.462 80 413 6.975 .98 100 2920 16230 50 60 147 157 0 39246 110 39136 6.311 34874 34764 .158 5.451 2.658 2.446
6 1563 888 79 106 1484 782 1160 631 83 109 1081 525 0 0 1257 597 29 33 100 100 98 100 2266 1606 1.898 .527 .486 1.05 .53 1.87 52 266 .473 .95 80 3090 16250 53 61 165 173 0 799 95 703 .474 568 472 2.11 .437 -1.077 -1.195
7 3448 1570 79 97 3369 1473 3750 1616 82 101 3671 1519 0 0 904 361 23 31 100 100 100 100 4842 5190 2.287 .437 .414 .45 .433 .09 80 469 .412 .98 110 3230 16220 48 59 177 188 0 1412 87 1325 .393 1454 1366 2.543 .372 -1.346 -1.426
8 4016 1100 84 98 3932 1002 4074 1156 88 101 3990 1058 0 0 2057 271 28 27 100 100 100 100 4934 5048 3.924 .255 .265 .339 .272 .225 52 346 .2 .91 90 3400 16230 50 59 195 204 0 989 88 901 .229 1040 952 4.362 .239 -2.125 -2.068
9 14114 684 83 101 14031 583 14710 672 87 104 14627 571 0 0 1901 146 25 26 100 100 100 100 14614 15198 24.067 .042 .039 .041 .041 .007 80 454 .041 .97 110 3570 16240 50 61 211 222 0 615 91 524 .037 604 514 26.755 .035 -4.742 -4.832
10 1075 687 80 104 995 583 1089 715 82 109 1009 611 0 0 294 186 22 29 100 100 100 100 1578 1620 1.707 .586 .606 .595 .606 .138 80 346 .56 .96 100 3730 16240 51 61 228 238 0 618 94 524 .527 643 550 1.897 .545 -.924 -.876
11 7644 10424 77 104 7567 10320 8453 11634 81 106 8376 11530 0 0 2891 3840 20 27 100 100 100 99 17887 19906 .733 1.364 1.377 1.779 1.375 2.503 120 471 1.331 .98 120 3890 16240 50 62 243 255 0 9377 94 9283 1.227 10465 10372 .815 1.238 .295 .308
12 841 1124 76 98 765 1026 836 1209 77 99 760 1111 0 0 200 285 18 24 100 100 100 100 1791 1871 .746 1.341 1.462 1.352 1.367 .283 80 397 1.303 .97 110 4050 16240 50 61 259 270 0 1011 88 923 1.206 1088 999 .829 1.315 .271 .395
13 4299 3737 74 97 4225 3640 4066 3720 77 98 3992 3623 0 0 2500 2065 20 24 100 100 100 100 7865 7615 1.161 .862 .908 .913 .845 .397 120 445 .834 .98 120 4210 16250 51 63 275 287 0 3362 87 3274 .775 3346 3259 1.29 .816 -.368 -.293
14 339 327 74 95 265 232 314 310 76 96 240 215 0 0 99 105 21 24 100 100 100 100 497 455 1.142 .875 .896 .914 .907 .335 80 367 .81 .87 100 4360 16240 51 61 291 301 0 294 85 209 .788 279 193 1.27 .806 -.345 -.311
15 852 689 73 97 779 592 792 631 75 99 719 534 0 0 269 205 22 25 100 100 100 100 1371 1253 1.316 .76 .743 .794 .744 .248 52 326 .692 .93 90 4520 16230 50 59 307 316 0 620 87 533 .684 568 480 1.463 .668 -.549 -.582
16 546 508 74 95 472 413 495 508 77 99 421 413 0 0 252 160 23 28 100 100 100 100 885 834 1.143 .875 .981 .966 .914 .393 80 400 .732 .92 100 4680 16240 51 61 323 333 0 457 85 372 .787 457 372 1.27 .882 -.345 -.18
17 11412 19359 75 99 11337 19260 12780 21113 77 101 12705 21014 0 0 4378 6750 18 24 100 100 100 100 30597 33719 .589 1.699 1.654 1.94 1.674 1.314 80 401 1.643 .98 100 4840 16240 51 61 339 349 0 17414 89 17325 1.528 18992 18903 .654 1.488 .612 .573
18 401 465 74 97 327 368 390 430 76 99 316 333 0 0 103 148 16 24 100 100 100 100 695 649 .889 1.125 1.054 1.185 1.086 .571 80 400 1.081 .93 100 5010 16240 51 61 356 366 0 418 87 331 1.012 387 300 .988 .948 .018 -.077
19 2110 2142 72 93 2038 2049 2114 2169 75 96 2042 2076 0 0 420 461 17 24 100 100 100 100 4087 4118 .995 1.005 1.017 1.013 1.024 .193 80 366 .979 .97 100 5170 16240 51 61 372 382 0 1927 84 1843 .904 1951 1867 1.106 .915 -.145 -.129
20 3812 1091 72 96 3740 995 3993 1169 76 99 3921 1073 0 0 1271 396 18 24 100 100 100 100 4735 4994 3.759 .266 .274 .267 .271 .076 120 490 .266 .98 120 5330 16240 50 62 387 399 0 981 86 895 .239 1052 965 4.179 .246 -2.063 -2.022

Total number of rows: 21504

Table truncated, full table size 4782 Kbytes.




Supplementary data files not provided
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