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Sample GSM94474 Query DataSets for GSM94474
Status Public on Feb 01, 2006
Title N2 vs CB4856
Sample type RNA
 
Channel 1
Source name N2
Organism Caenorhabditis elegans
Characteristics N2
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CB4856
Organism Caenorhabditis elegans
Characteristics CB4856
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: evolution, Thomas Strains
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42696.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 GPL3399
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 9138 18744 318 71 8820 18673 10090 20654 321 87 9772 20583 0 0 3508 7480 66 203 100 100 100 100 27493 30355 .472 2.117 2.106 2.138 2.136 1.361 120 550 2.16 .97 120 2260 17460 26 38 50 62 0 12774 48 12725 1.443 14075 14027 .693 1.435 .529 .521
2 1777 2486 301 72 1476 2414 2062 3020 340 102 1761 2948 0 0 973 1611 386 152 73 94 65 89 3890 4709 .611 1.636 1.674 1.64 1.663 1.668 156 605 1.68 .97 150 2430 17460 24 39 65 80 0 1694 49 1645 1.115 2058 2009 .897 1.141 .156 .19
3 455 320 270 74 185 246 447 323 293 114 177 249 0 0 78 87 108 213 83 75 33 0 431 426 .752 1.33 1.407 1.308 1.327 1.997 120 475 1.431 .68 130 2580 17450 24 37 81 94 0 218 50 168 .906 220 170 1.104 .959 -.142 -.061
4 465 524 262 74 203 450 423 495 266 90 161 421 0 0 170 124 62 177 96 100 66 78 653 582 .451 2.217 2.615 2.641 2.608 1.917 80 439 2.765 .65 110 2750 17440 24 35 99 110 0 357 50 307 1.511 337 287 .662 1.782 .595 .833
5 1898 2826 265 73 1633 2753 1931 2830 274 83 1666 2757 0 0 445 499 83 69 98 100 98 100 4386 4423 .593 1.686 1.655 1.785 1.629 1.492 120 579 1.651 .96 130 2920 17440 23 36 115 128 0 1926 50 1876 1.149 1929 1879 .87 1.128 .2 .173
6 7185 14781 246 71 6939 14710 7891 16242 280 85 7645 16171 0 0 2936 5833 334 83 91 100 90 100 21649 23816 .472 2.12 2.115 2.426 2.141 1.903 120 437 2.123 .98 120 3090 17440 24 36 133 145 0 10073 48 10024 1.445 11068 11020 .692 1.441 .531 .528
7 420 253 249 70 171 183 406 261 279 77 157 191 0 0 93 60 325 48 2 97 0 90 354 348 .934 1.07 1.217 1.169 1.142 1.933 120 448 .084 .39 120 3260 17440 24 36 150 162 0 172 48 125 .729 178 130 1.371 .829 -.455 -.27
8 607 585 276 72 331 513 609 600 279 75 333 528 0 0 132 158 55 23 99 100 98 100 844 861 .645 1.55 1.586 1.595 1.542 1.564 120 465 1.533 .86 120 3430 17440 24 36 167 179 0 399 49 350 1.056 409 360 .947 1.081 .079 .112
9 5577 7490 265 72 5312 7418 5631 7663 288 81 5366 7591 0 0 1001 1767 437 85 100 100 100 100 12730 12957 .716 1.396 1.415 1.368 1.417 1.254 120 477 1.403 .95 130 3600 17440 23 36 183 196 0 5104 49 5055 .952 5222 5173 1.051 .964 -.071 -.053
10 1733 1707 268 75 1465 1632 1750 1679 275 84 1482 1604 0 0 300 262 64 50 100 100 100 100 3097 3086 .898 1.114 1.082 1.124 1.102 1.274 80 378 1.102 .94 110 3760 17440 24 35 200 211 0 1163 51 1112 .759 1144 1093 1.317 .738 -.398 -.439
11 1676 2289 283 75 1393 2214 1675 2298 289 82 1392 2223 0 0 319 411 91 46 100 100 100 100 3607 3615 .629 1.589 1.597 1.605 1.549 1.263 80 422 1.59 .95 110 3940 17430 23 34 218 229 0 1560 51 1509 1.083 1566 1515 .923 1.088 .115 .122
12 1476 1992 252 77 1224 1915 1565 2161 275 89 1313 2084 0 0 334 641 218 62 97 98 95 96 3139 3397 .639 1.565 1.587 1.411 1.596 1.659 120 520 1.642 .96 120 4100 17440 24 36 234 246 0 1357 52 1305 1.066 1473 1420 .938 1.082 .092 .113
13 1615 2011 256 77 1359 1934 1435 2045 267 84 1179 1968 0 0 1315 404 140 47 100 100 100 100 3293 3147 .703 1.423 1.669 1.546 1.582 1.517 80 464 1.042 .62 110 4270 17440 24 35 251 262 0 1370 52 1318 .97 1394 1341 1.031 1.138 -.044 .186
14 749 817 274 73 475 744 710 798 278 83 436 725 0 0 239 182 46 96 100 100 100 100 1219 1161 .638 1.566 1.663 1.737 1.695 1.631 80 484 1.331 .84 110 4440 17430 23 34 268 279 0 557 50 507 1.067 544 494 .937 1.133 .094 .18
15 535 710 260 73 275 637 521 684 269 79 261 611 0 0 123 183 139 50 86 100 43 100 912 872 .432 2.316 2.341 2.483 2.312 1.57 80 496 .041 .13 110 4610 17430 23 34 285 296 0 484 50 434 1.579 466 416 .633 1.595 .659 .674
16 426 248 240 74 186 174 377 232 253 77 137 158 0 0 292 72 144 25 46 100 7 100 360 295 1.069 .935 1.153 1.188 1.149 2.171 80 462 .3 .45 110 4780 17430 23 34 302 313 0 169 50 119 .638 158 108 1.569 .786 -.649 -.348
17 901 948 266 74 635 874 873 846 273 80 607 772 0 0 327 893 165 49 94 100 90 100 1509 1379 .727 1.376 1.272 1.362 1.231 1.867 120 505 2.381 .53 120 4950 17430 23 35 319 331 0 646 50 596 .938 577 526 1.066 .867 -.092 -.206
18 940 957 277 75 663 882 945 954 287 81 668 879 0 0 187 192 174 51 98 100 96 100 1545 1547 .752 1.33 1.316 1.368 1.349 1.451 80 433 1.328 .91 110 5110 17430 23 34 335 346 0 652 51 601 .907 650 599 1.103 .897 -.142 -.157
19 520 372 281 76 239 296 474 315 284 79 193 239 0 0 243 184 47 24 92 100 86 97 535 432 .807 1.238 1.238 1.429 1.444 2.361 80 473 .897 .77 110 5290 17430 23 34 353 364 0 254 52 202 .844 215 163 1.185 .844 -.245 -.245
20 7794 18194 280 76 7514 18118 7965 18972 295 78 7685 18896 0 0 1103 3593 234 25 100 100 100 100 25632 26581 .415 2.411 2.459 2.353 2.49 1.295 120 521 2.48 .98 120 5460 17430 23 35 370 382 0 12399 52 12347 1.643 12929 12877 .609 1.676 .716 .745

Total number of rows: 20736

Table truncated, full table size 4610 Kbytes.




Supplementary data files not provided
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