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Sample GSM70921 Query DataSets for GSM70921
Status Public on Aug 20, 2005
Title Dauer MTC#4T8 (red, channel 2) vs. RefB-JW (green, channel 1)
Sample type RNA
 
Channel 1
Source name RefB-JW (green)
Organism Caenorhabditis elegans
Characteristics RefB-JW (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Dauer MTC#4T8 (red)
Organism Caenorhabditis elegans
Characteristics Dauer MTC#4T8 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10828.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 Aug 18, 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 GPL2653
Series (1)
GSE3169 Global analysis of dauer gene expression 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 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 11350 9777 537 560 10813 9217 null null 560 560 null null null null null null null null 100 100 null null null null 1.173 .852 null null .859 null 80 510 .837 .98 null null null 40 51 68 79 0 8428 482 7946 .735 null null 1.361 null -.444 null
2 3080 4879 538 550 2542 4329 null null 552 551 null null null null null null null null 98 100 null null null null .587 1.703 null null 1.76 null 80 456 1.616 .96 null null null 39 49 86 96 0 4206 474 3732 1.468 null null .681 null .554 null
3 1127 664 529 565 598 99 null null 555 565 null null null null null null null null 100 33 null null null null 6.04 .166 null null .092 null 12 104 .124 .25 null null null 41 46 104 109 0 572 487 85 .142 null null 7.035 null -2.815 null
4 3733 4670 570 555 3163 4115 null null 729 566 null null null null null null null null 43 100 null null null null .769 1.301 null null 1.329 null 80 436 .256 .45 null null null 38 48 118 128 0 4025 478 3547 1.121 null null .892 null .165 null
5 6978 7225 608 557 6370 6668 null null 801 562 null null null null null null null null 80 100 null null null null .955 1.047 null null 1.065 null 52 335 1.027 .97 null null null 40 49 133 142 0 6228 480 5748 .902 null null 1.108 null -.148 null
6 988 851 634 534 354 317 null null 648 558 null null null null null null null null 62 90 null null null null 1.117 .895 null null 1.39 null 32 165 .407 .58 null null null 40 46 154 160 0 733 460 273 .771 null null 1.297 null -.375 null
7 8315 7617 621 548 7694 7069 null null 648 558 null null null null null null null null 100 100 null null null null 1.088 .919 null null .917 null 52 348 .903 .98 null null null 39 48 166 175 0 6566 472 6094 .792 null null 1.263 null -.336 null
8 1137 931 629 536 508 395 null null 653 542 null null null null null null null null 67 82 null null null null 1.286 .778 null null .736 null 52 323 .603 .81 null null null 38 47 182 191 -100 802 462 340 .669 null null 1.494 null -.579 null
9 17023 1742 561 541 16462 1201 null null 606 548 null null null null null null null null 98 96 null null null null 13.707 .073 null null .072 null 156 723 .075 .96 null null null 36 50 196 210 0 1501 466 1035 .063 null null 15.905 null -3.991 null
10 1623 4110 525 538 1098 3572 null null 545 540 null null null null null null null null 91 100 null null null null .307 3.253 null null 3.421 null 120 568 2.937 .94 null null null 36 49 215 228 0 3543 463 3080 2.805 null null .356 null 1.488 null
11 7009 27592 509 503 6500 27089 null null 542 509 null null null null null null null null 100 100 null null null null .24 4.168 null null 4.169 null 52 290 3.725 .95 null null null 38 47 231 240 0 23786 433 23353 3.593 null null .278 null 1.845 null
12 2067 1391 501 490 1566 901 null null 521 494 null null null null null null null null 100 98 null null null null 1.738 .575 null null .591 null 52 284 .548 .91 null null null 40 48 248 256 0 1199 422 777 .496 null null 2.015 null -1.011 null
13 4737 8051 502 494 4235 7557 null null 514 500 null null null null null null null null 98 100 null null null null .56 1.784 null null 1.925 null 52 352 1.664 .96 null null null 38 47 262 271 0 6940 425 6515 1.538 null null .65 null .621 null
14 948 663 495 485 453 178 null null 514 486 null null null null null null null null 92 82 null null null null 2.545 .393 null null .431 null 52 309 .305 .62 null null null 39 47 280 288 0 571 418 153 .338 null null 2.961 null -1.566 null
15 1050 1052 492 496 558 556 null null 504 494 null null null null null null null null 92 100 null null null null 1.004 .996 null null .977 null 52 303 .735 .77 null null null 40 48 296 304 0 906 427 479 .858 null null 1.165 null -.22 null
16 1258 1306 500 509 758 797 null null 516 513 null null null null null null null null 100 100 null null null null .951 1.051 null null 1.051 null 52 323 .834 .83 null null null 39 48 311 320 0 1125 438 687 .906 null null 1.103 null -.142 null
17 5605 22544 497 486 5108 22058 null null 515 497 null null null null null null null null 96 100 null null null null .232 4.318 null null 4.328 null 80 393 4.235 .98 null null null 39 49 327 337 0 19434 418 19016 3.723 null null .269 null 1.896 null
18 1010 994 506 480 504 514 null null 519 485 null null null null null null null null 100 100 null null null null .981 1.02 null null .972 null 32 224 .801 .76 null null null 39 46 343 350 0 856 413 443 .879 null null 1.138 null -.186 null
19 3009 5233 505 463 2504 4770 null null 523 474 null null null null null null null null 100 100 null null null null .525 1.905 null null 1.895 null 52 352 1.811 .96 null null null 39 48 359 368 0 4511 399 4112 1.642 null null .609 null .716 null
20 6151 1695 493 477 5658 1218 null null 509 480 null null null null null null null null 100 100 null null null null 4.645 .215 null null .211 null 52 370 .192 .93 null null null 37 46 375 384 0 1461 411 1050 .186 null null 5.389 null -2.43 null

Total number of rows: 21504

Table truncated, full table size 5235 Kbytes.




Supplementary data files not provided
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