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Sample GSM70925 Query DataSets for GSM70925
Status Public on Aug 20, 2005
Title L1 MTC#2T3 (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 L1 MTC#2T3 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#2T3 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13805.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 5325 7775 95 86 5230 7689 6994 10047 99 89 6899 9961 0 0 3631 5103 37 31 100 100 100 100 12919 16860 .68 1.47 1.444 1.77 1.444 1.123 52 372 1.333 .96 90 1890 19680 39 48 88 97 0 5933 66 5868 1.122 7667 7601 .891 1.102 .166 .14
2 1510 4375 93 87 1417 4288 1720 5183 95 90 1627 5096 0 0 737 2323 25 24 98 100 97 100 5705 6723 .33 3.026 3.132 3.384 3.145 1.937 80 464 2.943 .96 100 2060 19690 40 50 105 115 0 3339 66 3272 2.309 3955 3889 .433 2.39 1.207 1.257
3 308 235 95 84 213 151 313 234 97 86 218 150 0 0 64 94 26 23 100 87 100 84 364 368 1.411 .709 .688 .708 .701 .372 32 231 .654 .8 70 2220 19700 42 49 122 129 0 179 64 115 .541 179 114 1.848 .525 -.886 -.929
4 2448 3017 97 88 2351 2929 1938 2583 104 92 1841 2495 0 0 1676 2160 31 26 100 100 100 100 5280 4336 .803 1.246 1.355 1.424 1.19 1.169 52 318 1.23 .97 80 2380 19700 42 50 138 146 0 2302 67 2235 .951 1971 1904 1.052 1.034 -.073 .049
5 6330 2598 100 87 6230 2511 3917 1539 105 89 3817 1452 0 0 4618 1982 31 24 100 100 100 100 8741 5269 2.481 .403 .38 .449 .379 .319 52 322 .399 .96 80 2540 19700 42 50 154 162 0 1983 66 1916 .308 1174 1108 3.251 .29 -1.701 -1.784
6 196 150 99 91 97 59 165 139 103 93 66 48 0 0 99 53 31 27 68 71 53 46 156 114 1.644 .608 .727 1.901 .703 5.463 32 176 .338 .52 60 2710 19700 43 49 172 178 0 114 69 45 .464 106 37 2.154 .555 -1.107 -.849
7 4251 1855 105 90 4146 1765 4617 2057 130 108 4512 1967 0 0 1935 862 275 174 94 96 94 92 5911 6479 2.349 .426 .436 .503 .433 .441 52 312 .413 .95 80 2860 19700 42 50 186 194 0 1416 69 1347 .325 1570 1501 3.078 .333 -1.622 -1.588
8 1037 453 114 82 923 371 853 416 121 84 739 334 0 0 619 202 38 21 100 100 100 100 1294 1073 2.488 .402 .452 .512 .456 .266 32 176 .318 .84 60 3010 19700 43 49 202 208 0 346 63 283 .307 317 255 3.26 .345 -1.705 -1.536
9 11500 815 107 87 11393 728 13960 646 117 89 13853 559 0 0 7497 535 48 24 100 100 100 99 12121 14412 15.65 .064 .04 .065 .065 .027 120 691 .064 .96 130 3180 19690 38 51 215 228 0 622 66 556 .049 493 427 20.508 .031 -4.358 -5.021
10 1234 933 102 94 1132 839 1294 971 109 96 1192 877 0 0 327 255 36 26 98 100 98 100 1971 2069 1.349 .741 .736 .803 .736 .424 52 290 .719 .96 80 3350 19700 42 50 235 243 0 712 72 640 .566 741 669 1.768 .561 -.822 -.833
11 6009 15129 101 94 5908 15035 6925 17659 105 96 6824 17565 0 0 2658 6464 28 27 100 100 100 100 20943 24389 .393 2.545 2.574 3.713 2.483 3.948 52 301 2.435 .97 80 3510 19700 42 50 251 259 0 11545 72 11473 1.942 13476 13404 .515 1.964 .958 .974
12 952 2293 100 91 852 2202 951 2325 103 94 851 2234 0 0 291 838 27 25 100 100 100 100 3054 3085 .387 2.585 2.625 2.691 2.599 1.002 52 293 2.467 .94 80 3670 19700 42 50 267 275 0 1750 69 1680 1.972 1774 1705 .507 2.003 .98 1.002
13 3366 4828 100 98 3266 4730 3981 5537 104 101 3881 5439 0 0 1561 2266 30 27 100 100 100 100 7996 9320 .69 1.448 1.401 1.647 1.447 .832 32 230 1.412 .97 70 3820 19700 42 49 282 289 0 3684 75 3610 1.105 4225 4151 .905 1.069 .144 .097
14 381 326 98 93 283 233 386 318 102 97 288 225 0 0 108 96 34 29 98 100 98 98 516 513 1.215 .823 .781 .904 .857 .433 52 315 .739 .89 80 3990 19700 42 50 299 307 0 249 71 178 .628 243 172 1.592 .596 -.671 -.746
15 749 801 96 86 653 715 733 819 99 90 637 733 0 0 326 342 26 31 100 100 100 100 1368 1370 .913 1.095 1.151 1.231 1.13 .666 52 307 .983 .91 80 4150 19710 43 51 315 323 0 611 66 546 .836 625 559 1.197 .878 -.259 -.188
16 550 821 102 99 448 722 524 804 110 108 422 705 0 0 160 128 48 42 100 100 100 100 1170 1127 .62 1.612 1.671 1.847 1.551 .834 32 230 1.228 .9 70 4310 19700 42 49 331 338 0 627 76 551 1.23 614 538 .813 1.275 .298 .35
17 7020 19855 105 97 6915 19758 9127 22032 108 102 9022 21935 0 0 3923 10845 35 31 100 100 100 100 26673 30957 .35 2.857 2.431 6.583 2.885 14.473 52 310 2.742 .97 80 4460 19700 42 50 346 354 0 15152 74 15078 2.18 16813 16739 .459 1.855 1.125 .892
18 472 638 100 91 372 547 482 645 103 94 382 554 0 0 124 166 29 24 96 100 96 100 919 936 .68 1.47 1.45 1.738 1.458 1.624 52 308 1.323 .9 80 4630 19700 42 50 363 371 0 487 69 417 1.122 492 423 .891 1.107 .166 .146
19 1598 3426 99 90 1499 3336 1684 3803 103 94 1585 3713 0 0 631 1136 28 26 98 100 92 100 4835 5298 .449 2.225 2.343 4.713 2.298 9.259 52 358 2.061 .96 90 4790 19700 41 50 378 387 0 2614 69 2546 1.698 2902 2833 .589 1.788 .764 .838
20 3672 1603 101 89 3571 1514 4005 1689 104 95 3904 1600 0 0 1218 470 33 30 100 100 100 100 5085 5504 2.359 .424 .41 .503 .427 .518 52 360 .399 .96 90 4950 19700 41 50 394 403 0 1223 68 1155 .324 1289 1221 3.091 .313 -1.628 -1.677

Total number of rows: 21504

Table truncated, full table size 4780 Kbytes.




Supplementary data files not provided
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