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Sample GSM93985 Query DataSets for GSM93985
Status Public on Jan 28, 2006
Title 11a (control) (red, channel 2) vs. 11b (clofibrate) (green, channel 1)
Sample type RNA
 
Channel 1
Source name 11b (clofibrate) (green, channel 1)
Organism Caenorhabditis elegans
Characteristics 11b (clofibrate) (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 11a (control) (red, channel 2)
Organism Caenorhabditis elegans
Characteristics 11a (control) (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16443.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 27, 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)
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 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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 766 517 55 456 711 61 813 517 59 482 758 61 0 0 294 249 25 211 100 30 96 7 772 819 11.656 .086 .08 .819 .291 2.155 80 407 .064 .1 100 2420 18480 23 33 81 91 0 573 505 68 .095 573 68 10.522 .089 -3.395 -3.488
2 221 495 58 441 163 54 209 481 66 474 151 40 0 0 82 222 32 227 98 20 92 5 217 191 3.019 .331 .265 1.596 1.299 1.6 80 389 .178 .06 100 2590 18480 23 33 98 108 0 548 489 60 .367 533 44 2.725 .293 -1.446 -1.769
3 74 453 57 453 17 0 68 419 61 476 11 -34 0 0 23 179 24 236 37 11 7 1 17 -23 null null null 12.209 6.143 14.628 80 392 .286 .03 100 2750 18480 23 33 114 124 0 502 502 0 null 464 -38 null null null null
4 599 536 56 452 543 84 589 539 61 481 533 87 0 0 162 235 27 235 100 28 100 3 627 620 6.464 .155 .163 .527 .417 .347 52 316 .052 .05 90 2910 18480 23 32 130 139 0 594 501 93 .171 597 96 5.836 .181 -2.545 -2.467
5 464 577 57 428 407 149 499 530 59 464 442 102 0 0 195 270 22 226 93 33 92 15 556 544 2.732 .366 .231 1.048 .599 1.286 80 393 .196 .16 100 3070 18470 22 32 146 156 0 639 474 165 .406 587 113 2.466 .256 -1.302 -1.968
6 72 487 60 469 12 18 66 480 72 493 6 11 0 0 32 188 49 226 11 13 5 1 30 17 .667 1.5 1.833 12.939 5.614 16.443 80 379 .531 .1 100 3230 18480 23 33 162 172 0 539 520 20 1.662 532 12 .602 2.031 .733 1.022
7 447 597 64 484 383 113 407 550 82 595 343 66 0 0 158 257 110 976 98 1 88 0 496 409 3.389 .295 .192 .781 .5 .854 80 378 .854 .16 100 3390 18480 23 33 178 188 0 661 536 125 .327 609 73 3.06 .213 -1.613 -2.23
8 165 570 62 480 103 90 156 530 70 592 94 50 0 0 90 260 105 1019 43 0 16 0 193 144 1.144 .874 .532 7.143 2.176 12.312 80 348 .357 .03 100 3550 18480 23 33 194 204 0 631 532 100 .968 587 55 1.033 .589 -.047 -.763
9 1293 1163 65 480 1228 683 1245 899 77 502 1180 419 0 0 874 728 46 230 84 67 80 47 1911 1599 1.798 .556 .355 2.953 .547 11.172 208 816 .602 .83 160 3720 18510 23 39 208 224 0 1288 532 757 .616 996 464 1.623 .393 -.699 -1.346
10 172 561 69 478 103 83 166 530 98 503 97 52 0 0 82 286 81 223 60 30 18 13 186 149 1.241 .806 .536 9.14 2.63 18.62 80 331 .19 .05 100 3860 18480 23 33 225 235 0 621 530 92 .893 587 58 1.12 .594 -.164 -.752
11 750 526 72 468 678 58 757 457 150 495 685 -11 0 0 237 276 171 222 100 25 86 9 736 674 11.69 .086 null .64 .31 .96 52 294 -1 -1 90 4040 18460 21 30 243 252 0 583 518 64 .095 506 -12 10.553 null -3.4 null
12 120 524 63 460 57 64 109 491 108 489 46 31 0 0 50 220 137 219 10 23 0 5 121 77 .891 1.123 .674 8.744 3.436 16.105 80 366 -.133 -.06 100 4180 18480 23 33 257 267 0 580 510 71 1.244 544 34 .804 .747 .315 -.422
13 142 544 59 464 83 80 78 539 65 489 19 75 0 0 127 217 44 228 37 23 31 3 163 94 1.038 .964 3.947 10.128 2.792 17.892 80 408 .155 .06 100 4340 18480 23 33 273 283 0 603 514 89 1.068 597 83 .937 4.373 .095 2.129
14 91 501 57 481 34 20 80 496 59 494 23 15 0 0 41 238 17 220 56 12 38 6 54 38 1.7 .588 .652 11.668 5.315 16.058 80 378 .257 .03 100 4500 18480 23 33 289 299 0 555 533 22 .652 549 17 1.535 .722 -.618 -.469
15 107 504 57 459 50 45 88 480 60 481 31 21 0 0 61 262 17 206 62 25 47 11 95 52 1.111 .9 .677 7.409 4.431 8.743 80 378 .81 .14 100 4660 18480 23 33 305 315 0 558 508 50 .997 532 23 1.003 .75 -.004 -.414
16 109 534 60 464 49 70 96 510 62 493 36 46 0 0 51 216 19 226 68 21 47 5 119 82 .7 1.429 1.278 9.995 3.836 16.496 80 384 .319 .05 100 4820 18480 23 33 321 331 0 592 514 78 1.582 565 51 .632 1.415 .662 .501
17 701 619 61 473 640 146 723 598 64 499 662 125 0 0 442 261 27 221 84 32 83 11 786 787 4.384 .228 .189 4.5 .32 14.118 156 579 .182 .3 140 5000 18500 23 37 337 351 0 686 524 162 .253 662 138 3.957 .209 -1.984 -2.257
18 102 513 59 480 43 33 92 464 62 514 33 -16 0 0 48 257 17 231 72 20 47 6 76 17 1.303 .767 null 10.138 6.787 11.251 80 361 .189 .03 100 5140 18480 23 33 353 363 0 568 532 37 .85 514 -18 1.176 null -.234 null
19 456 653 65 475 391 178 461 599 92 502 396 124 0 0 261 270 84 213 80 40 75 15 569 520 2.197 .455 .313 2.806 .728 6.213 52 290 .264 .23 80 5330 18480 24 32 373 381 0 723 526 197 .504 664 137 1.983 .347 -.988 -1.528
20 744 792 67 468 677 324 776 770 99 501 709 302 0 0 332 357 92 222 92 58 92 30 1001 1011 2.09 .479 .426 1.458 .57 4.082 120 434 .446 .53 120 5500 18500 24 36 388 400 0 877 518 359 .53 853 335 1.886 .472 -.916 -1.084

Total number of rows: 21504

Table truncated, full table size 4572 Kbytes.




Supplementary data files not provided
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