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Sample GSM85232 Query DataSets for GSM85232
Status Public on Nov 26, 2005
Title 8a (control) (red, channel 2) vs. 8b (B-naphthoflavone) (green, channel 1)
Sample type RNA
 
Channel 1
Source name 8b (B-naphthoflavone) (green, channel 1)
Organism Caenorhabditis elegans
Characteristics 8b (B-naphthoflavone) (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 8a (control) (red, channel 2)
Organism Caenorhabditis elegans
Characteristics 8a (control) (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14316.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 GPL2655
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 4067 981 83 383 3984 598 2770 808 95 387 2687 425 0 0 3677 558 114 77 83 75 80 63 4582 3112 6.662 .15 .158 .612 .164 2.4 120 545 .142 .93 120 1490 19300 64 76 51 63 0 1330 519 811 .204 1096 576 4.913 .214 -2.297 -2.221
2 593 656 82 374 511 282 673 646 93 383 591 272 0 0 267 165 86 74 88 91 83 76 793 863 1.812 .552 .46 .96 .545 1.773 80 372 .481 .81 110 1660 19300 64 75 68 79 0 890 507 382 .748 876 369 1.336 .624 -.418 -.68
3 131 313 81 377 50 -64 125 307 90 384 44 -70 0 0 48 93 79 74 21 11 2 0 -14 -26 null null null 3.611 1.315 6.714 80 433 .218 .23 110 1820 19290 63 74 84 95 0 424 511 -87 null 416 -95 null null null null
4 1940 719 81 384 1859 335 2297 702 84 384 2216 318 0 0 952 194 24 63 100 93 100 81 2194 2534 5.549 .18 .144 .261 .18 .281 80 411 .17 .86 110 1980 19300 64 75 100 111 0 975 521 454 .244 952 431 4.092 .195 -2.033 -2.361
5 1957 1562 83 378 1874 1184 1168 1022 89 380 1085 644 0 0 1840 1249 26 67 82 75 77 67 3058 1729 1.583 .632 .594 1.592 .643 4.757 120 532 .636 .96 120 2150 19290 63 75 117 129 0 2118 513 1606 .857 1386 873 1.167 .805 -.223 -.313
6 145 501 83 377 62 124 109 433 87 381 26 56 0 0 85 164 27 74 48 46 34 34 186 82 .5 2 2.154 5.268 1.929 9.176 52 238 1.35 .63 80 2310 19270 63 71 135 143 0 679 511 168 2.712 587 76 .369 2.921 1.439 1.546
7 1245 793 80 382 1165 411 1441 774 83 383 1361 392 0 0 1005 364 24 70 79 74 72 62 1576 1753 2.835 .353 .288 2.314 .369 6.314 120 487 .328 .91 120 2470 19290 63 75 149 161 0 1075 518 557 .478 1050 532 2.09 .391 -1.064 -1.356
8 615 612 77 393 538 219 567 558 80 400 490 165 0 0 371 233 19 64 95 73 95 56 757 655 2.457 .407 .337 .589 .485 .686 80 276 .401 .75 100 2630 19290 64 74 166 176 0 830 533 297 .552 757 224 1.812 .457 -.857 -1.131
9 3995 5232 77 388 3918 4844 3145 4070 80 393 3068 3682 0 0 2993 4037 21 69 93 94 90 92 8762 6750 .809 1.236 1.2 1.727 1.255 2.923 156 600 1.251 .97 150 2770 19290 61 76 177 192 0 7095 526 6569 1.677 5519 4993 .596 1.627 .746 .703
10 673 480 77 374 596 106 826 473 80 375 749 99 0 0 372 100 26 66 95 65 93 37 702 848 5.623 .178 .132 .348 .197 1.013 120 332 .163 .63 120 2950 19290 63 75 197 209 0 651 507 144 .241 641 134 4.146 .179 -2.052 -2.48
11 4845 1164 78 375 4767 789 5090 1126 82 378 5012 751 0 0 3073 559 24 68 97 89 93 83 5556 5763 6.042 .166 .15 .613 .171 3.553 156 538 .165 .95 150 3100 19270 59 74 210 225 0 1578 509 1070 .224 1527 1018 4.455 .203 -2.156 -2.299
12 249 518 81 390 168 128 246 508 83 394 165 118 0 0 137 131 23 70 83 64 68 42 296 283 1.313 .762 .715 1.733 .88 3.18 156 462 .635 .64 140 3260 19280 61 75 227 241 0 702 529 174 1.033 689 160 .968 .97 .047 -.044
13 2347 920 82 407 2265 513 1218 606 84 411 1136 199 0 0 2442 599 24 68 82 66 73 55 2778 1335 4.415 .226 .175 .615 .237 1.051 120 399 .228 .95 120 3430 19280 62 74 245 257 0 1248 552 696 .307 822 270 3.256 .238 -1.703 -2.074
14 191 381 81 412 110 -31 191 383 84 416 110 -29 0 0 96 91 22 69 72 8 67 3 79 81 null null null 3.318 .54 6.204 80 400 -.242 -.21 110 3580 19270 61 72 260 271 0 517 559 -42 null 519 -39 null null null null
15 263 383 81 400 182 -17 282 375 85 404 201 -25 0 0 120 97 22 67 83 13 81 7 165 176 null null null 1.184 .325 2.6 80 444 -.032 -.04 110 3740 19270 61 72 276 287 0 519 542 -23 null 509 -34 null null null null
16 324 457 79 400 245 57 342 435 81 401 263 35 0 0 170 138 21 64 83 40 83 27 302 298 4.298 .233 .133 1.288 .432 2.478 80 364 .254 .34 100 3910 19270 62 72 294 304 0 620 542 77 .315 590 47 3.17 .18 -1.664 -2.47
17 4098 2171 78 393 4020 1778 3844 1925 83 395 3766 1532 0 0 3673 1591 27 63 85 84 81 78 5798 5298 2.261 .442 .407 2.953 .487 10.577 120 438 .421 .96 120 4070 19270 61 73 309 321 0 2944 533 2411 .6 2610 2078 1.667 .552 -.737 -.858
18 219 483 82 400 137 83 234 487 93 405 152 87 0 0 131 127 45 115 55 38 55 11 220 239 1.651 .606 .572 3.4 .737 9.906 52 278 .343 .34 90 4200 19250 60 69 323 332 0 655 542 113 .822 660 118 1.217 .776 -.284 -.366
19 1288 700 82 400 1206 300 1446 628 92 404 1364 228 0 0 1071 342 54 97 69 57 67 54 1506 1592 4.02 .249 .167 2.041 .287 7.551 120 477 .312 .75 120 4380 19270 61 73 340 352 0 949 542 407 .337 852 309 2.964 .227 -1.568 -2.141
20 1392 1531 79 395 1313 1136 1264 1287 88 400 1185 892 0 0 979 873 56 77 85 91 83 85 2449 2077 1.156 .865 .753 1.543 .836 3.15 156 572 .837 .95 140 4540 19270 60 74 355 369 0 2076 536 1541 1.173 1745 1210 .852 1.021 .231 .03

Total number of rows: 21504

Table truncated, full table size 4684 Kbytes.




Supplementary data files not provided
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