NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM85231 Query DataSets for GSM85231
Status Public on Nov 26, 2005
Title 4a (N2 control) (red, channel 2) vs. 4b (B-naphthoflavone) (green, channel 1)
Sample type RNA
 
Channel 1
Source name 4b (B-naphthoflavone) (green)
Organism Caenorhabditis elegans
Characteristics 4b (B-naphthoflavone) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 4a (N2 control) (red)
Organism Caenorhabditis elegans
Characteristics 4a (N2 control) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6844.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 Nov 25, 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 GPL3097
Series (2)
GSE3680 Beta-naphthoflavone treated worms
GSE4111 Expression profiling of five different xenobiotics using a C. elegans microarray

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
1 467 477 154 297 313 180 null null 163 307 null null null null null null null null 66 48 null null null null 1.739 .575 null null .668 null 80 395 .504 .76 null null null 82 92 95 105 0 781 486 295 .942 null null 1.061 null -.085 null
2 340 374 164 280 176 94 null null 174 286 null null null null null null null null 51 36 null null null null 1.872 .534 null null .901 null 52 313 .226 .41 null null null 82 90 112 120 0 613 459 154 .875 null null 1.143 null -.193 null
3 652 269 170 296 482 null null null 179 299 null null null null null null null null 98 7 null null null null null null null null .391 null 52 252 .095 .25 null null null 84 92 133 141 0 440 485 null null null null null null null null
4 1050 712 163 281 887 431 null null 222 312 null null null null null null null null 23 47 null null null null 2.058 .486 null null .496 null 80 401 .342 .85 null null null 79 90 141 152 0 1167 460 707 .797 null null 1.255 null -.327 null
5 627 573 155 278 472 295 null null 157 286 null null null null null null null null 85 62 null null null null 1.6 .625 null null .712 null 120 502 .458 .78 null null null 80 92 157 169 0 939 455 484 1.025 null null .975 null .036 null
6 336 505 155 277 181 228 null null 156 284 null null null null null null null null 65 55 null null null null .794 1.26 null null 1.781 null 80 365 .915 .77 null null null 79 89 176 186 0 827 454 373 2.061 null null .485 null 1.043 null
7 507 561 158 284 349 277 null null 160 297 null null null null null null null null 62 35 null null null null 1.26 .794 null null 1.005 null 120 469 .701 .8 null null null 79 91 190 202 0 919 465 454 1.301 null null .769 null .379 null
8 455 645 159 283 296 362 null null 160 286 null null null null null null null null 67 61 null null null null .818 1.223 null null 1.531 null 52 331 .704 .68 null null null 81 90 208 217 0 1057 463 594 2.007 null null .498 null 1.005 null
9 417 627 156 278 261 349 null null 156 282 null null null null null null null null 82 73 null null null null .748 1.337 null null 1.754 null 52 198 .795 .75 null null null 83 91 225 233 0 1027 455 572 2.192 null null .456 null 1.132 null
10 791 769 155 278 636 491 null null 157 282 null null null null null null null null 92 61 null null null null 1.295 .772 null null .881 null 120 351 .726 .86 null null null 81 93 237 249 0 1260 455 805 1.266 null null .79 null .34 null
11 604 776 156 282 448 494 null null 157 288 null null null null null null null null 78 72 null null null null .907 1.103 null null 1.352 null 80 325 .87 .86 null null null 80 91 253 264 0 1272 462 810 1.808 null null .553 null .854 null
12 1066 1014 159 274 907 740 null null 160 284 null null null null null null null null 86 89 null null null null 1.226 .816 null null .856 null 156 600 .732 .9 null null null 78 93 268 283 0 1662 449 1213 1.337 null null .748 null .419 null
13 298 576 163 270 135 306 null null 165 276 null null null null null null null null 60 63 null null null null .441 2.267 null null 2.258 null 156 638 1.365 .66 null null null 79 94 285 300 0 944 442 502 3.719 null null .269 null 1.895 null
14 299 517 165 276 134 241 null null 168 280 null null null null null null null null 71 63 null null null null .556 1.799 null null 2.335 null 80 319 1.382 .69 null null null 81 91 305 315 0 847 452 395 2.948 null null .339 null 1.56 null
15 295 458 165 277 130 181 null null 166 277 null null null null null null null null 72 72 null null null null .718 1.392 null null 1.917 null 80 364 .905 .7 null null null 81 92 319 330 0 750 454 296 2.277 null null .439 null 1.187 null
16 239 414 162 272 77 142 null null 237 396 null null null null null null null null 0 0 null null null null .542 1.844 null null 2.286 null 80 339 1.189 .65 null null null 81 91 337 347 -100 678 445 233 3.026 null null .33 null 1.597 null
17 597 502 161 265 436 237 null null 454 860 null null null null null null null null 3 0 null null null null 1.84 .544 null null .527 null 80 340 1.868 .92 null null null 81 92 351 362 0 822 434 388 .89 null null 1.124 null -.168 null
18 350 466 160 262 190 204 null null 163 267 null null null null null null null null 67 62 null null null null .931 1.074 null null 1.815 null 80 334 .476 .51 null null null 83 93 368 378 0 763 429 334 1.758 null null .569 null .814 null
19 713 745 159 251 554 494 null null 160 259 null null null null null null null null 82 75 null null null null 1.121 .892 null null 1.128 null 52 195 .503 .63 null null null 84 92 386 394 0 1221 411 810 1.462 null null .684 null .548 null
20 1371 891 160 254 1211 637 null null 161 257 null null null null null null null null 87 70 null null null null 1.901 .526 null null .574 null 80 284 .459 .88 null null null 82 92 400 410 0 1460 416 1044 .862 null null 1.16 null -.214 null

Total number of rows: 21504

Table truncated, full table size 5128 Kbytes.




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