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Sample GSM94429 Query DataSets for GSM94429
Status Public on Feb 01, 2006
Title N2-III (starting line) (red, channel 2) vs. MA59-III (no selection) (green, channel 1)
Sample type RNA
 
Channel 1
Source name MA59-III (no selection) (green)
Organism Caenorhabditis elegans
Characteristics MA59-III (no selection) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2-III (starting line) (red)
Organism Caenorhabditis elegans
Characteristics N2-III (starting line) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: evolution, Thomas Strains
Image: http://smd.stanford.edu/MicroArray/gifs/2000-01/1827.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 30, 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 GPL3098
Series (1)
GSE4123 The transcriptional consequences of mutation and natural selection 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 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
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 1169 1817 209 81 960 1736 null null 210 85 null null null null null null null null 86 98 null null null null .553 1.808 null null 1.686 null 52 344 1.47 .853 null null null 50 59 59 68 0 1289 57 1231 1.283 null null .78 null .359 null
2 709 819 211 79 498 740 null null 211 83 null null null null null null null null 90 10 null null null null .673 1.486 null null 1.545 null 52 342 1.229 .838 null null null 50 59 76 85 0 581 56 525 1.054 null null .949 null .076 null
3 538 415 206 76 332 339 null null 209 78 null null null null null null null null 75 84 null null null null .979 1.021 null null .946 null 52 345 .772 .743 null null null 49 58 92 101 0 294 54 240 .724 null null 1.381 null -.466 null
4 1059 2422 207 77 852 2345 null null 209 80 null null null null null null null null 84 98 null null null null .363 2.752 null null 2.487 null 52 361 2.139 .838 null null null 49 58 108 117 0 1718 55 1663 1.952 null null .512 null .965 null
5 1548 3647 202 74 1346 3573 null null 204 78 null null null null null null null null 10 10 null null null null .377 2.655 null null 2.368 null 52 327 2.339 .867 null null null 48 57 126 135 0 2587 52 2534 1.883 null null .531 null .913 null
6 885 1098 203 75 682 1023 null null 204 77 null null null null null null null null 84 10 null null null null .667 1.5 null null 1.294 null 52 307 1.125 .807 null null null 48 57 140 149 0 779 53 726 1.064 null null .94 null .089 null
7 991 1682 208 75 783 1607 null null 211 78 null null null null null null null null 92 98 null null null null .487 2.052 null null 2.174 null 156 690 1.649 .843 null null null 46 60 155 169 0 1193 53 1140 1.456 null null .687 null .542 null
8 602 665 218 76 384 589 null null 219 78 null null null null null null null null 88 86 null null null null .652 1.534 null null 1.195 null 52 304 1.254 .809 null null null 48 57 173 182 0 472 54 418 1.088 null null .919 null .121 null
9 477 507 209 81 268 426 null null 207 82 null null null null null null null null 73 90 null null null null .629 1.59 null null 1.313 null 52 345 1.101 .699 null null null 47 56 189 198 0 360 57 302 1.127 null null .887 null .173 null
10 1047 1725 204 76 843 1649 null null 203 82 null null null null null null null null 98 10 null null null null .511 1.956 null null 1.846 null 52 320 1.627 .837 null null null 47 56 205 214 0 1223 54 1170 1.387 null null .721 null .472 null
11 557 478 204 80 353 398 null null 206 85 null null null null null null null null 10 98 null null null null .887 1.127 null null .92 null 120 522 .994 .771 null null null 45 57 221 233 0 339 57 282 .8 null null 1.251 null -.323 null
12 2839 4102 202 99 2637 4003 null null 207 103 null null null null null null null null 10 10 null null null null .659 1.518 null null 1.521 null 52 310 1.348 .871 null null null 45 54 238 247 0 2909 70 2839 1.077 null null .929 null .106 null
13 1486 2894 208 117 1278 2777 null null 212 122 null null null null null null null null 96 10 null null null null .46 2.173 null null 2.146 null 52 332 1.686 .836 null null null 46 55 253 262 0 2052 83 1969 1.541 null null .649 null .624 null
14 980 1442 208 106 772 1336 null null 213 117 null null null null null null null null 96 10 null null null null .578 1.731 null null 1.29 null 52 341 1.273 .699 null null null 46 55 270 279 0 1023 75 948 1.227 null null .815 null .296 null
15 892 1278 208 109 684 1169 null null 210 117 null null null null null null null null 98 10 null null null null .585 1.709 null null 1.506 null 52 344 1.295 .758 null null null 45 54 286 295 0 906 77 829 1.212 null null .825 null .278 null
16 700 1151 206 133 494 1018 null null 208 141 null null null null null null null null 90 10 null null null null .485 2.061 null null 1.927 null 52 333 1.428 .778 null null null 45 54 302 311 -100 816 94 722 1.462 null null .684 null .547 null
17 1551 2946 215 149 1336 2797 null null 218 155 null null null null null null null null 10 10 null null null null .478 2.094 null null 2.068 null 52 342 1.845 .885 null null null 44 53 318 327 0 2089 106 1984 1.485 null null .673 null .57 null
18 618 767 222 161 396 606 null null 225 162 null null null null null null null null 96 10 null null null null .653 1.53 null null 1.468 null 52 336 1.081 .735 null null null 43 52 334 343 0 544 114 430 1.085 null null .921 null .118 null
19 807 979 219 129 588 850 null null 220 132 null null null null null null null null 92 90 null null null null .692 1.446 null null 1.413 null 52 334 1.274 .831 null null null 43 52 349 358 0 694 91 603 1.025 null null .975 null .036 null
20 1894 4854 212 80 1682 4774 null null 216 85 null null null null null null null null 10 10 null null null null .352 2.838 null null 2.8 null 52 344 2.603 .892 null null null 43 52 366 375 0 3443 57 3386 2.013 null null .497 null 1.009 null

Total number of rows: 21120

Table truncated, full table size 5021 Kbytes.




Supplementary data files not provided
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