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Sample GSM94441 Query DataSets for GSM94441
Status Public on Feb 01, 2006
Title N2-II (starting line) (red, channel 2) vs. PB306-II (with selection) (green, channel 1)
Sample type RNA
 
Channel 1
Source name PB306-II (with selection) (green)
Organism Caenorhabditis elegans
Characteristics PB306-II (with selection) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2-II (starting line) (red)
Organism Caenorhabditis elegans
Characteristics N2-II (starting line) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: evolution, Thomas Strains
Image: http://smd.stanford.edu/MicroArray/gifs/2000-01/1723.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
1 723 539 192 101 531 438 null null 203 109 null null null null null null null null 56 52 null null null null 1.212 .825 null null .572 null 120 512 .491 .592 null null null 88 100 50 62 0 657 123 534 1.006 null null .994 null .008 null
2 463 304 211 106 252 198 null null 221 115 null null null null null null null null 45 42 null null null null 1.273 .786 null null .639 null 120 356 .413 .529 null null null 87 99 66 78 0 371 129 242 .96 null null 1.041 null -.058 null
3 335 170 211 120 124 50 null null 219 128 null null null null null null null null 38 24 null null null null 2.48 .403 null null .833 null 120 348 .21 .354 null null null 87 99 82 94 0 207 146 61 .492 null null 2.033 null -1.023 null
4 897 703 213 115 684 588 null null 217 122 null null null null null null null null 55 44 null null null null 1.163 .86 null null .871 null 120 358 .551 .64 null null null 87 99 98 110 0 857 140 717 1.048 null null .954 null .068 null
5 1089 1227 208 115 881 1112 null null 214 122 null null null null null null null null 60 64 null null null null .792 1.262 null null 1.229 null 120 350 .829 .702 null null null 87 99 114 126 0 1496 140 1356 1.539 null null .65 null .622 null
6 368 161 209 115 159 46 null null 219 119 null null null null null null null null 41 37 null null null null 3.457 .289 null null .393 null 120 330 .141 .381 null null null 86 98 130 142 0 196 140 56 .352 null null 2.839 null -1.506 null
7 3091 3272 221 119 2870 3153 null null 229 123 null null null null null null null null 90 92 null null null null .91 1.099 null null 1.033 null 156 519 .868 .808 null null null 84 99 143 158 0 3990 145 3845 1.34 null null .746 null .422 null
8 409 235 226 120 183 115 null null 234 126 null null null null null null null null 37 38 null null null null 1.591 .628 null null .782 null 120 367 .356 .534 null null null 86 98 162 174 0 287 146 141 .77 null null 1.298 null -.376 null
9 309 136 215 117 94 19 null null 222 124 null null null null null null null null 39 15 null null null null 4.947 .202 null null .417 null 120 370 .07 .155 null null null 85 97 178 190 0 166 143 23 .245 null null 4.087 null -2.031 null
10 797 476 221 121 576 355 null null 229 131 null null null null null null null null 57 53 null null null null 1.623 .616 null null .434 null 120 353 .453 .732 null null null 85 97 194 206 0 580 148 432 .75 null null 1.333 null -.415 null
11 634 510 234 123 400 387 null null 242 130 null null null null null null null null 78 87 null null null null 1.034 .968 null null .827 null 120 353 .635 .663 null null null 85 97 210 222 0 622 150 472 1.18 null null .847 null .239 null
12 989 2399 231 119 758 2280 null null 238 133 null null null null null null null null 69 77 null null null null .332 3.008 null null 2.381 null 120 350 2.076 .703 null null null 85 97 226 238 0 2926 145 2781 3.669 null null .273 null 1.875 null
13 478 343 226 119 252 224 null null 244 133 null null null null null null null null 40 51 null null null null 1.125 .889 null null .59 null 120 356 .357 .5 null null null 84 96 242 254 0 418 145 273 1.083 null null .923 null .115 null
14 368 177 224 118 144 59 null null 240 128 null null null null null null null null 38 27 null null null null 2.441 .41 null null .493 null 120 348 .139 .288 null null null 84 96 258 270 0 216 144 72 .5 null null 2 null -1 null
15 449 211 211 118 238 93 null null 223 122 null null null null null null null null 56 50 null null null null 2.559 .391 null null .508 null 120 348 .242 .526 null null null 84 96 274 286 0 257 144 113 .475 null null 2.106 null -1.075 null
16 532 286 217 118 315 168 null null 227 122 null null null null null null null null 51 52 null null null null 1.875 .533 null null .712 null 120 371 .391 .644 null null null 84 96 290 302 -100 349 144 205 .651 null null 1.537 null -.62 null
17 1425 993 245 117 1180 876 null null 249 123 null null null null null null null null 59 73 null null null null 1.347 .742 null null .754 null 120 365 .517 .722 null null null 85 97 306 318 0 1211 143 1068 .905 null null 1.105 null -.144 null
18 514 266 253 112 261 154 null null 261 124 null null null null null null null null 59 51 null null null null 1.695 .59 null null .425 null 120 378 .32 .48 null null null 85 97 322 334 0 324 137 187 .716 null null 1.396 null -.481 null
19 542 336 244 113 298 223 null null 257 123 null null null null null null null null 44 54 null null null null 1.336 .748 null null .669 null 120 370 .45 .645 null null null 85 97 338 350 0 410 138 272 .913 null null 1.096 null -.132 null
20 1916 1526 237 119 1679 1407 null null 252 125 null null null null null null null null 65 60 null null null null 1.193 .838 null null .775 null 120 381 .552 .674 null null null 84 96 354 366 0 1861 145 1716 1.022 null null .978 null .031 null

Total number of rows: 21120

Table truncated, full table size 5041 Kbytes.




Supplementary data files not provided
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