NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM94427 Query DataSets for GSM94427
Status Public on Feb 01, 2006
Title N2 II (starting line) (red, channel 2) vs. MA96 II (no selection) (green, channel 1)
Sample type RNA
 
Channel 1
Source name MA96 II (no selection) (green)
Organism Caenorhabditis elegans
Characteristics MA96 II (no selection) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 II (starting line) (red)
Organism Caenorhabditis elegans
Characteristics N2 II (starting line) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: evolution, Thomas Strains
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6858.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 GPL3096
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 1001 1628 351 336 650 1292 null null 360 354 null null null null null null null null 48 55 null null null null .503 1.988 null null 1.729 null 52 339 1.42 .82 null null null 207 216 130 139 0 1292 266 1026 1.578 null null .634 null .659 null
2 660 1185 347 335 313 850 null null 352 341 null null null null null null null null 36 51 null null null null .368 2.716 null null .971 null 52 351 1.531 .63 null null null 205 214 148 157 0 940 265 675 2.157 null null .464 null 1.109 null
3 731 1187 347 339 384 848 null null 348 350 null null null null null null null null 26 42 null null null null .453 2.208 null null .75 null 52 269 1.303 .82 null null null 207 215 164 172 0 942 269 673 1.753 null null .571 null .81 null
4 625 1387 358 357 267 1030 null null 363 365 null null null null null null null null 23 35 null null null null .259 3.858 null null 1.063 null 80 487 1.798 .66 null null null 200 211 179 190 0 1100 283 817 3.06 null null .327 null 1.613 null
5 843 920 346 359 497 561 null null 365 378 null null null null null null null null 48 34 null null null null .886 1.129 null null 1.476 null 52 337 1.164 .87 null null null 204 213 196 205 0 730 284 446 .897 null null 1.114 null -.156 null
6 653 1028 356 366 297 662 null null 374 377 null null null null null null null null 30 42 null null null null .449 2.229 null null 1.537 null 52 307 1.383 .76 null null null 204 212 213 221 0 815 290 525 1.768 null null .566 null .822 null
7 1298 1664 371 353 927 1311 null null 381 369 null null null null null null null null 61 62 null null null null .707 1.414 null null 1.184 null 80 503 1.288 .91 null null null 201 212 229 240 0 1320 280 1040 1.122 null null .891 null .166 null
8 964 2022 371 342 593 1680 null null 375 345 null null null null null null null null 36 53 null null null null .353 2.833 null null .955 null 52 285 2.052 .88 null null null 205 214 245 254 0 1604 271 1333 2.248 null null .445 null 1.169 null
9 476 685 375 357 101 328 null null 384 384 null null null null null null null null 15 15 null null null null .308 3.248 null null .7 null 80 516 1.096 .58 null null null 200 211 259 270 0 543 283 260 2.574 null null .388 null 1.364 null
10 927 1736 422 457 505 1279 null null 427 487 null null null null null null null null 42 51 null null null null .395 2.533 null null 2.233 null 52 257 1.725 .78 null null null 207 215 279 287 0 1377 362 1015 2.01 null null .498 null 1.007 null
11 1295 1942 459 512 836 1430 null null 476 547 null null null null null null null null 51 61 null null null null .585 1.711 null null 1.639 null 52 318 1.471 .9 null null null 202 211 292 301 0 1541 406 1135 1.358 null null .737 null .441 null
12 1017 972 427 428 590 544 null null 443 456 null null null null null null null null 43 42 null null null null 1.085 .922 null null 1.089 null 80 364 .886 .81 null null null 203 213 309 319 0 771 339 432 .732 null null 1.366 null -.45 null
13 1070 1944 448 469 622 1475 null null 459 502 null null null null null null null null 66 71 null null null null .422 2.371 null null 1.703 null 156 748 1.883 .83 null null null 200 215 322 337 0 1542 372 1170 1.881 null null .532 null .912 null
14 949 1535 472 524 477 1011 null null 483 537 null null null null null null null null 56 65 null null null null .472 2.119 null null 1.877 null 52 267 1.713 .89 null null null 202 210 342 350 0 1218 415 803 1.683 null null .594 null .751 null
15 764 1161 481 506 283 655 null null 494 524 null null null null null null null null 56 69 null null null null .432 2.314 null null 2.157 null 52 302 1.31 .7 null null null 203 212 356 365 0 921 401 520 1.837 null null .544 null .878 null
16 1307 2601 437 450 870 2151 null null 457 489 null null null null null null null null 56 75 null null null null .404 2.472 null null 2.313 null 80 477 1.892 .87 null null null 201 212 370 381 -100 2064 357 1707 1.962 null null .51 null .972 null
17 1923 3080 426 466 1497 2614 null null 437 488 null null null null null null null null 65 69 null null null null .573 1.746 null null 1.607 null 120 570 1.571 .9 null null null 201 214 387 400 0 2444 369 2075 1.386 null null .721 null .471 null
18 1371 2716 442 511 929 2205 null null 455 537 null null null null null null null null 41 47 null null null null .421 2.374 null null 1.788 null 120 428 1.945 .89 null null null 202 214 406 418 0 2155 405 1750 1.884 null null .531 null .914 null
19 755 1305 429 490 326 815 null null 444 503 null null null null null null null null 32 46 null null null null .4 2.5 null null 1.629 null 80 324 1.707 .8 null null null 203 213 420 430 0 1035 388 647 1.985 null null .504 null .989 null
20 1429 3028 431 481 998 2547 null null 445 500 null null null null null null null null 50 67 null null null null .392 2.552 null null 2.762 null 52 334 2.07 .86 null null null 203 212 436 445 0 2403 381 2022 2.026 null null .494 null 1.019 null

Total number of rows: 20736

Table truncated, full table size 4969 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap