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Sample GSM94448 Query DataSets for GSM94448
Status Public on Feb 01, 2006
Title "MA83-2(B) (red, channel 2) vs. MA99-2(A) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA99-2(A) (green)
Organism Caenorhabditis elegans
Characteristics MA99-2(A) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA83-2(B) (red)
Organism Caenorhabditis elegans
Characteristics MA83-2(B) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16491.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 2173 865 65 372 2108 493 2391 749 67 391 2326 377 0 0 1613 519 23 179 95 63 92 51 2601 2703 4.276 .234 .162 .589 .263 1.624 120 556 .225 .76 120 2160 18620 69 81 53 65 0 1138 490 649 .308 986 496 3.249 .213 -1.7 -2.229
2 1215 1085 65 381 1150 704 1222 1075 68 401 1157 694 0 0 864 602 23 180 94 74 92 61 1854 1851 1.634 .612 .6 1.215 .611 2.766 120 436 .575 .85 120 2330 18610 68 80 70 82 0 1428 501 927 .806 1415 913 1.241 .789 -.312 -.341
3 798 918 65 387 733 531 690 724 67 401 625 337 0 0 725 545 22 174 80 69 70 49 1264 962 1.38 .724 .539 3.063 .789 6.08 120 418 .619 .81 120 2500 18610 68 80 87 99 0 1208 509 699 .953 953 444 1.049 .71 -.069 -.495
4 1402 711 65 395 1337 316 651 549 67 407 586 154 0 0 1491 457 21 186 78 46 74 36 1653 740 4.231 .236 .263 3.469 .338 11.392 120 368 .234 .75 120 2660 18630 70 82 103 115 0 936 520 416 .311 723 203 3.215 .346 -1.685 -1.532
5 2736 819 65 380 2671 439 1823 667 68 397 1758 287 0 0 2815 549 22 187 78 61 75 41 3110 2045 6.084 .164 .163 2.847 .188 7.581 120 471 .157 .78 130 2830 18620 68 81 119 132 0 1078 500 578 .216 878 378 4.623 .215 -2.209 -2.219
6 379 685 67 378 312 307 122 542 69 393 55 164 0 0 470 406 21 196 71 42 55 36 619 219 1.016 .984 2.982 4.964 1.492 9.205 52 212 .756 .7 80 2980 18610 70 78 137 145 0 902 497 404 1.295 713 216 .772 3.924 .373 1.972
7 1172 995 68 389 1104 606 1155 864 69 401 1087 475 0 0 883 594 19 174 97 66 95 57 1710 1562 1.822 .549 .437 1.246 .595 4.101 120 442 .557 .86 120 3130 18610 68 80 150 162 0 1310 512 798 .722 1137 625 1.384 .575 -.469 -.798
8 703 747 69 379 634 368 419 641 72 394 350 262 0 0 701 440 21 170 70 61 63 44 1002 612 1.723 .58 .749 5.212 .671 14.358 120 379 .516 .79 120 3300 18610 68 80 167 179 0 983 499 484 .764 844 345 1.309 .985 -.389 -.022
9 9173 1014 69 393 9104 621 6756 778 71 416 6687 385 0 0 8348 727 23 173 89 62 84 51 9725 7072 14.66 .068 .058 1.206 .077 3.867 156 556 .069 .84 150 3460 18610 66 81 181 196 0 1335 517 817 .09 1024 507 11.139 .076 -3.478 -3.722
10 1076 1020 67 387 1009 633 1092 900 70 409 1025 513 0 0 909 605 21 180 86 69 80 59 1642 1538 1.594 .627 .5 2.237 .743 6.151 120 364 .554 .82 120 3630 18610 68 80 200 212 0 1342 509 833 .826 1184 675 1.211 .659 -.276 -.602
11 2574 934 67 376 2507 558 2828 871 69 389 2761 495 0 0 1856 493 21 175 97 71 95 57 3065 3256 4.493 .223 .179 1.388 .239 5.805 120 410 .219 .84 130 3780 18610 67 80 214 227 0 1229 495 734 .293 1146 651 3.414 .236 -1.771 -2.083
12 995 1029 65 374 930 655 783 889 69 394 718 515 0 0 858 629 20 183 87 71 83 52 1585 1233 1.42 .704 .717 2.299 .844 5.527 120 426 .644 .85 130 3940 18620 68 81 230 243 0 1354 492 862 .927 1170 678 1.079 .944 -.109 -.083
13 1734 927 62 380 1672 547 937 747 126 462 875 367 0 0 1770 632 630 535 55 43 45 18 2219 1242 3.057 .327 .419 3.022 .407 12.661 80 380 .31 .84 110 4100 18610 68 79 247 258 0 1220 500 720 .431 983 483 2.323 .552 -1.216 -.857
14 636 855 61 382 575 473 426 764 113 439 365 382 0 0 539 532 571 485 43 41 20 18 1048 747 1.216 .823 1.047 4.332 .932 13.336 80 463 .786 .79 110 4250 18600 67 78 262 273 0 1125 503 623 1.083 1006 503 .924 1.377 .115 .462
15 752 930 63 385 689 545 486 726 65 399 423 341 0 0 657 587 20 169 82 66 81 51 1234 764 1.264 .791 .806 1.627 .88 3.796 80 447 .755 .83 110 4430 18600 67 78 280 291 0 1224 507 717 1.041 955 449 .961 1.061 .058 .085
16 919 849 63 374 856 475 789 726 66 397 726 352 0 0 786 486 21 176 91 60 87 49 1331 1078 1.802 .555 .485 1.017 .602 1.209 120 478 .513 .81 120 4580 18610 68 80 295 307 0 1117 492 625 .73 955 463 1.369 .638 -.453 -.648
17 3225 770 63 380 3162 390 2468 637 66 397 2405 257 0 0 2933 522 21 163 93 57 90 42 3552 2662 8.108 .123 .107 .505 .139 1.273 80 391 .126 .74 110 4750 18610 68 79 312 323 0 1013 500 513 .162 838 338 6.16 .141 -2.623 -2.83
18 956 1030 62 387 894 643 871 791 64 403 809 404 0 0 819 692 20 183 90 63 83 52 1537 1213 1.39 .719 .499 1.616 .794 4.589 120 436 .714 .87 120 4920 18600 67 79 329 341 0 1356 509 846 .947 1041 532 1.056 .657 -.079 -.606
19 1192 891 62 393 1130 498 962 814 65 407 900 421 0 0 981 497 20 178 93 70 90 54 1628 1321 2.269 .441 .468 1.853 .5 5.052 120 357 .418 .82 120 5070 18610 68 80 344 356 0 1173 517 655 .58 1071 554 1.724 .616 -.786 -.7
20 2447 859 64 385 2383 474 1531 695 66 400 1467 310 0 0 2125 586 20 177 87 57 80 48 2857 1777 5.027 .199 .211 2.24 .225 8.337 156 501 .214 .83 140 5220 18610 67 81 358 372 0 1131 507 624 .262 915 408 3.82 .278 -1.934 -1.846

Total number of rows: 21504

Table truncated, full table size 4730 Kbytes.




Supplementary data files not provided
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