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Sample GSM70939 Query DataSets for GSM70939
Status Public on Aug 20, 2005
Title Dauer MTC#3T2 (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#3T2 (red)
Organism Caenorhabditis elegans
Characteristics Dauer MTC#3T2 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11167.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 2397 1204 106 106 2291 1098 null null 106 108 null null null null null null null null 99 99 null null null null 2.087 .479 null null 2.176 null 120 638 .452 .95 null null null 58 71 27 40 0 1416 124 1292 .564 null null 1.773 null -.826 null
2 1049 1820 108 109 941 1711 null null 109 111 null null null null null null null null 100 100 null null null null .55 1.818 null null .55 null 120 554 1.749 .96 null null null 59 71 45 57 0 2141 128 2013 2.139 null null .467 null 1.097 null
3 331 240 108 105 223 135 null null 110 111 null null null null null null null null 100 96 null null null null 1.652 .605 null null 1.48 null 32 224 .523 .8 null null null 61 68 64 71 0 282 123 159 .713 null null 1.403 null -.488 null
4 3026 2436 103 108 2923 2328 null null 106 112 null null null null null null null null 100 100 null null null null 1.256 .796 null null 1.311 null 52 305 .763 .94 null null null 61 69 79 87 0 2865 127 2738 .937 null null 1.068 null -.094 null
5 4384 2044 103 108 4281 1936 null null 105 110 null null null null null null null null 100 100 null null null null 2.211 .452 null null 2.158 null 52 385 .421 .96 null null null 58 67 94 103 0 2404 127 2277 .532 null null 1.88 null -.911 null
6 831 496 104 112 727 384 null null 112 115 null null null null null null null null 100 100 null null null null 1.893 .528 null null 1.322 null 12 68 .381 .82 null null null 62 66 113 117 0 583 131 452 .622 null null 1.608 null -.686 null
7 3393 1376 108 113 3285 1263 null null 119 117 null null null null null null null null 100 100 null null null null 2.601 .384 null null 2.619 null 80 466 .372 .96 null null null 58 69 126 137 0 1618 132 1486 .452 null null 2.211 null -1.144 null
8 848 673 110 115 738 558 null null 112 125 null null null null null null null null 98 98 null null null null 1.323 .756 null null 1.34 null 52 250 .707 .93 null null null 58 66 143 151 0 791 135 656 .889 null null 1.125 null -.17 null
9 8236 3057 111 113 8125 2944 null null 114 119 null null null null null null null null 100 100 null null null null 2.76 .362 null null 2.757 null 120 632 .357 .96 null null null 55 68 156 169 0 3596 132 3464 .426 null null 2.346 null -1.23 null
10 1433 1877 112 115 1321 1762 null null 117 121 null null null null null null null null 100 100 null null null null .75 1.334 null null .746 null 52 212 1.255 .95 null null null 59 67 175 183 0 2208 135 2073 1.569 null null .637 null .65 null
11 8042 13826 110 111 7932 13715 null null 119 116 null null null null null null null null 100 100 null null null null .578 1.729 null null .602 null 156 774 1.791 .96 null null null 55 69 186 200 0 16265 130 16135 2.034 null null .492 null 1.024 null
12 933 527 116 112 817 415 null null 129 117 null null null null null null null null 100 97 null null null null 1.969 .508 null null 2.02 null 80 397 .481 .93 null null null 57 67 206 216 0 620 131 489 .599 null null 1.671 null -.741 null
13 5570 6549 113 108 5457 6441 null null 115 112 null null null null null null null null 100 100 null null null null .847 1.18 null null .794 null 52 289 1.145 .95 null null null 58 66 222 230 0 7704 127 7577 1.388 null null .72 null .474 null
14 439 400 112 113 327 287 null null 115 114 null null null null null null null null 100 98 null null null null 1.139 .878 null null 1.146 null 52 300 .818 .94 null null null 58 66 239 247 0 470 132 338 1.034 null null .967 null .048 null
15 2110 1521 109 110 2001 1411 null null 112 112 null null null null null null null null 100 100 null null null null 1.418 .705 null null 1.38 null 52 312 .618 .93 null null null 57 65 254 262 0 1789 129 1660 .83 null null 1.205 null -.27 null
16 746 905 107 116 639 789 null null 113 126 null null null null null null null null 100 100 null null null null .81 1.235 null null .805 null 52 362 1.074 .92 null null null 56 65 270 279 0 1064 136 928 1.452 null null .689 null .538 null
17 11240 21607 111 114 11129 21493 null null 123 127 null null null null null null null null 100 100 null null null null .518 1.931 null null .488 null 52 344 1.881 .97 null null null 56 65 285 294 0 25420 134 25286 2.272 null null .44 null 1.184 null
18 715 1034 112 115 603 919 null null 121 124 null null null null null null null null 100 100 null null null null .656 1.524 null null .65 null 52 290 1.412 .94 null null null 57 65 302 310 0 1216 135 1081 1.793 null null .558 null .842 null
19 3464 4509 114 115 3350 4394 null null 118 118 null null null null null null null null 100 100 null null null null .762 1.312 null null .727 null 52 332 1.311 .95 null null null 56 65 317 326 0 5304 135 5169 1.543 null null .648 null .626 null
20 6550 1508 108 113 6442 1395 null null 113 117 null null null null null null null null 100 100 null null null null 4.618 .217 null null 4.604 null 120 539 .224 .96 null null null 53 65 333 345 0 1774 132 1642 .255 null null 3.923 null -1.972 null

Total number of rows: 21504

Table truncated, full table size 5175 Kbytes.




Supplementary data files not provided
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