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Sample GSM69760 Query DataSets for GSM69760
Status Public on Aug 13, 2005
Title "mutant sorted touch cell (red, channel 2) vs. wt sorted touch cell (repeat #4) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name wt sorted touch cell (green)
Organism Caenorhabditis elegans
Characteristics wt sorted touch cell (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name mutant sorted touch cell (red)
Organism Caenorhabditis elegans
Characteristics mutant sorted touch cell (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17048.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 12, 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 GPL2754
Series (1)
GSE3121 Identification of genes expressed in C. elegans touch receptor neurons

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
1 297 412 98 349 199 63 251 389 105 365 153 40 0 0 188 235 41 160 73 25 62 13 262 193 3.159 .317 .261 2.546 1.193 6.211 80 432 .426 .33 100 1650 18480 452 462 138 148 0 446 377 68 .342 421 43 2.92 .283 -1.546 -1.822
2 345 471 94 348 251 123 310 423 102 361 216 75 0 0 212 260 40 156 85 35 75 21 374 291 2.041 .49 .347 2.045 .829 5.056 80 395 .506 .41 100 1810 18470 451 461 154 164 0 509 376 133 .53 458 81 1.887 .376 -.916 -1.413
3 375 526 97 350 278 176 385 506 103 368 288 156 0 0 139 233 42 163 96 48 96 21 454 444 1.58 .633 .542 1.037 .884 .951 52 340 .592 .44 90 1970 18470 451 460 170 179 0 569 379 190 .685 547 169 1.46 .586 -.546 -.771
4 377 669 99 364 278 305 377 613 102 398 278 249 0 0 220 293 43 253 76 48 75 25 583 527 .911 1.097 .896 3.887 1.013 7.037 52 297 .757 .53 80 2150 18460 451 459 189 197 0 724 394 330 1.187 663 269 .843 .969 .247 -.046
5 402 564 93 353 309 211 320 520 100 387 227 167 0 0 289 306 43 231 77 41 63 21 520 394 1.464 .683 .736 2.891 .812 8.686 80 459 .535 .44 110 2300 18470 450 461 202 213 0 610 382 228 .739 562 181 1.354 .796 -.437 -.33
6 188 418 101 362 87 56 150 398 104 379 49 36 0 0 114 191 41 168 51 30 40 11 143 85 1.554 .644 .735 7.991 2.356 16.256 52 322 .126 .04 90 2470 18470 451 460 220 229 0 452 392 61 .696 430 39 1.436 .795 -.522 -.332
7 380 468 99 365 281 103 388 459 106 376 289 94 0 0 171 193 59 168 86 40 82 10 384 383 2.728 .367 .325 1.078 .666 1.349 80 433 .381 .32 110 2620 18470 450 461 234 245 0 506 395 111 .396 496 102 2.522 .352 -1.335 -1.507
8 410 504 94 342 316 162 428 475 98 363 334 133 0 0 226 257 37 164 87 45 82 23 478 467 1.951 .513 .398 1.93 .631 3.941 80 386 .549 .5 100 2780 18470 451 461 251 261 0 545 370 175 .555 514 144 1.803 .431 -.851 -1.215
9 736 617 97 357 639 260 796 581 100 374 699 224 0 0 333 287 40 156 92 56 90 43 899 923 2.458 .407 .32 .57 .47 .476 80 436 .414 .59 110 2940 18470 450 461 266 277 0 667 386 281 .44 628 242 2.272 .347 -1.184 -1.529
10 475 593 93 371 382 222 496 540 99 379 403 169 0 0 233 268 44 154 96 51 85 35 604 572 1.721 .581 .419 1.024 .744 1.113 80 442 .564 .52 110 3100 18470 450 461 282 293 0 641 401 240 .629 584 183 1.591 .454 -.67 -1.141
11 452 664 101 376 351 288 469 693 149 408 368 317 0 0 226 299 722 237 5 57 0 30 639 685 1.219 .821 .861 1.489 .98 1.662 52 328 .224 .62 90 3270 18470 451 460 300 309 0 718 407 312 .888 750 343 1.127 .932 -.172 -.102
12 404 597 102 381 302 216 384 539 148 415 282 158 0 0 212 281 727 243 5 42 0 19 518 440 1.398 .715 .56 2.04 .788 4.19 52 319 .218 .62 90 3420 18470 451 460 315 324 0 646 412 234 .774 583 171 1.293 .606 -.37 -.723
13 111 335 95 380 16 -45 103 327 103 387 8 -53 0 0 45 127 41 162 28 3 12 3 -29 -45 null null null 10.481 5.684 13.084 32 219 -.347 -.08 70 3560 18470 452 459 330 337 -100 362 411 -49 null 354 -57 null null null null
14 553 635 96 418 457 217 466 599 104 439 370 181 0 0 649 280 49 166 94 53 84 30 674 551 2.106 .475 .489 2.268 .81 8.154 52 381 .194 .31 90 3750 18460 450 459 348 357 0 687 452 235 .514 648 196 1.947 .529 -.961 -.918
15 431 664 101 457 330 207 405 592 107 466 304 135 0 0 250 279 52 171 81 46 75 31 537 439 1.594 .627 .444 1.732 .806 3.693 80 400 .66 .53 100 3910 18470 451 461 364 374 0 718 494 224 .678 640 146 1.474 .48 -.56 -1.058
16 462 650 101 474 361 176 488 588 108 501 387 114 0 0 268 317 44 192 82 38 76 22 537 501 2.051 .488 .295 1.416 .744 2.07 80 424 .496 .44 100 4070 18460 450 460 380 390 0 703 513 190 .527 636 123 1.896 .319 -.923 -1.65
17 1440 1031 102 538 1338 493 1513 1045 110 546 1411 507 0 0 480 403 46 190 100 69 100 61 1831 1918 2.714 .368 .359 .419 .379 .318 52 341 .369 .65 90 4230 18460 450 459 396 405 0 1115 582 533 .399 1130 548 2.509 .389 -1.327 -1.363
18 495 663 108 608 387 55 488 643 117 623 380 35 0 0 280 304 52 211 83 30 76 10 442 415 7.036 .142 .092 1.633 .456 2.853 80 409 .358 .31 100 4390 18470 451 461 412 422 0 717 658 59 .154 696 38 6.505 .1 -2.702 -3.327
19 599 717 108 614 491 103 606 721 115 640 498 107 0 0 259 325 48 223 92 34 90 15 594 605 4.767 .21 .215 1.958 .488 4.801 52 329 .26 .24 90 4550 18460 450 459 428 437 0 776 664 111 .227 780 116 4.407 .232 -2.14 -2.105
20 479 739 114 705 365 34 521 690 121 736 407 -15 0 0 259 347 47 243 81 22 80 8 399 392 10.735 .093 null 1.992 .585 5.498 80 400 .318 .23 100 4700 18460 450 460 443 453 0 799 763 37 .101 746 -16 9.925 null -3.311 null

Total number of rows: 21504

Table truncated, full table size 4702 Kbytes.




Supplementary data files not provided
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