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Sample GSM94453 Query DataSets for GSM94453
Status Public on Feb 01, 2006
Title "MA99-3(A) (red, channel 2) vs. MA83-3(B) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA83-3(B) (green)
Organism Caenorhabditis elegans
Characteristics MA83-3(B) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA99-3(A) (red)
Organism Caenorhabditis elegans
Characteristics MA99-3(A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16494.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 Jan 30, 2006
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)
GSE4123 The transcriptional consequences of mutation and natural selection 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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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 2711 1739 87 132 2624 1607 3487 1686 90 136 3400 1554 0 0 1738 1201 30 37 96 95 95 93 4231 4954 1.633 .612 .457 .729 .598 .982 120 628 .621 .96 130 1660 18940 100 113 57 70 0 1292 98 1194 .455 1252 1154 2.198 .339 -1.136 -1.559
2 935 820 95 137 840 683 982 747 99 138 887 610 0 0 596 585 30 35 88 84 83 77 1523 1497 1.23 .813 .688 .985 .787 1.412 156 528 .846 .94 140 1840 18940 100 114 75 89 0 609 102 507 .604 555 453 1.656 .511 -.728 -.969
3 236 370 80 130 156 240 183 259 83 132 103 129 0 0 179 285 26 34 66 70 56 63 396 232 .65 1.538 1.252 2.854 1.552 4.878 120 430 1.439 .91 130 2000 18950 101 114 91 104 0 275 97 178 1.143 192 96 .875 .93 .192 -.104
4 1551 1496 77 127 1474 1369 1677 1417 80 129 1600 1290 0 0 982 976 27 35 88 93 85 90 2843 2890 1.077 .929 .806 1.28 .898 1.601 80 358 .924 .97 110 2160 18950 102 113 108 119 0 1111 94 1017 .69 1053 958 1.45 .599 -.536 -.74
5 1880 2588 76 131 1804 2457 1407 1720 80 133 1331 1589 0 0 1726 2438 25 35 80 85 76 80 4261 2920 .734 1.362 1.194 1.839 1.355 1.674 120 487 1.357 .98 120 2330 18950 102 114 125 137 0 1922 97 1825 1.012 1278 1180 .988 .887 .017 -.173
6 363 482 75 132 288 350 154 272 79 133 79 140 0 0 415 403 27 35 73 88 51 75 638 219 .823 1.215 1.772 2.659 1.341 4.352 52 275 .969 .93 90 2500 18940 102 111 143 152 0 358 98 260 .903 202 104 1.108 1.316 -.148 .397
7 948 866 77 133 871 733 783 637 81 136 706 504 0 0 744 674 26 37 84 79 80 75 1604 1210 1.188 .842 .714 1.188 .854 1.772 156 560 .845 .96 140 2640 18950 101 115 155 169 0 643 99 544 .625 473 374 1.6 .53 -.678 -.915
8 496 631 81 136 415 495 432 567 85 139 351 431 0 0 357 400 26 37 83 82 78 80 910 782 .838 1.193 1.228 1.53 1.213 1.707 120 423 1.081 .92 130 2800 18940 100 113 171 184 0 469 101 368 .886 421 320 1.129 .912 -.175 -.133
9 9148 7112 83 135 9065 6977 6774 5461 88 138 6691 5326 0 0 7161 6137 35 38 87 90 84 89 16042 12017 1.299 .77 .796 1.047 .763 1.907 156 536 .792 .97 150 2960 18950 100 115 186 201 0 5283 100 5182 .572 4056 3956 1.749 .591 -.807 -.758
10 452 493 83 132 369 361 337 379 86 134 254 247 0 0 341 363 34 37 75 76 69 68 730 501 1.022 .978 .972 2.228 1.049 6.884 120 394 .973 .94 130 3120 18950 101 114 203 216 0 366 98 268 .727 282 183 1.376 .722 -.461 -.469
11 3041 1393 82 129 2959 1264 2867 1152 84 132 2785 1023 0 0 2203 1091 25 36 86 83 83 80 4223 3808 2.341 .427 .367 .891 .428 2.659 156 539 .442 .96 150 3290 18950 100 115 219 234 0 1035 96 939 .317 856 760 3.152 .273 -1.656 -1.874
12 410 496 77 127 333 369 345 394 80 131 268 267 0 0 305 361 25 34 75 68 67 64 702 535 .902 1.108 .996 1.496 1.154 1.722 156 464 1.074 .93 140 3460 18950 101 115 237 251 0 368 94 274 .823 293 198 1.215 .74 -.281 -.434
13 1283 948 76 131 1207 817 394 392 79 134 318 261 0 0 1427 1024 24 35 75 72 69 65 2024 579 1.477 .677 .821 1.744 .683 4.411 120 360 .672 .95 120 3610 18950 102 114 253 265 0 704 97 607 .503 291 194 1.989 .61 -.992 -.714
14 234 339 76 130 158 209 194 236 80 132 118 106 0 0 157 232 23 36 70 65 58 56 367 224 .756 1.323 .898 1.951 1.451 1.879 120 416 1.289 .89 120 3770 18950 102 114 269 281 0 252 97 155 .983 175 79 1.018 .667 -.025 -.584
15 264 339 79 132 185 207 193 255 289 389 114 123 0 0 204 252 908 898 0 0 0 0 392 237 .894 1.119 1.079 2.78 1.194 5.574 120 408 1.054 .87 120 3930 18950 102 114 285 297 0 252 98 154 .831 189 91 1.203 .801 -.267 -.319
16 776 676 79 139 697 537 478 618 482 706 399 479 0 0 2946 477 1606 1343 1 3 0 0 1234 878 1.298 .77 1.201 1.369 1.186 1.357 156 512 .17 .31 140 4100 18950 101 115 301 315 0 502 103 399 .572 459 356 1.747 .892 -.805 -.165
17 1875 1892 74 127 1801 1765 1388 1550 163 294 1314 1423 0 0 1721 1659 445 831 59 56 55 46 3566 2737 1.02 .98 1.083 2.363 .999 4.697 120 367 .939 .97 130 4260 18950 101 114 317 330 0 1405 94 1311 .728 1151 1057 1.374 .804 -.458 -.314
18 449 611 74 125 375 486 375 543 76 128 301 418 0 0 361 479 21 35 80 73 66 64 861 719 .772 1.296 1.389 1.862 1.348 3.129 156 459 1.273 .96 140 4420 18940 100 114 333 347 0 454 93 361 .963 403 310 1.039 1.031 -.055 .045
19 1070 970 73 126 997 844 1237 1153 75 130 1164 1027 0 0 680 621 21 37 89 85 87 80 1841 2191 1.181 .847 .882 .798 .796 .317 120 396 .831 .95 130 4560 18940 100 113 347 360 0 720 94 627 .629 856 763 1.59 .655 -.669 -.61
20 2142 1699 73 132 2069 1567 2206 1573 76 136 2133 1441 0 0 1587 1329 24 37 84 83 82 82 3636 3574 1.32 .757 .676 1.26 .787 3.327 156 489 .767 .96 140 4740 18940 100 114 365 379 0 1262 98 1164 .563 1168 1070 1.778 .502 -.83 -.995

Total number of rows: 21504

Table truncated, full table size 4710 Kbytes.




Supplementary data files not provided
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