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Sample GSM94428 Query DataSets for GSM94428
Status Public on Feb 01, 2006
Title N2-I (starting line) (red,channel 2)vs PB306-I (with selection) (green,channel 1)
Sample type RNA
 
Channel 1
Source name PB306-I (with selection) (green)
Organism Caenorhabditis elegans
Characteristics PB306-I (with selection) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2-I (starting line) (red)
Organism Caenorhabditis elegans
Characteristics N2-I (starting line) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: evolution, Thomas Strains
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2730.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 5908 3109 117 112 5791 2997 null null 132 126 null null null null null null null null 98 98 null null null null 1.932 .518 null null .526 null 52 324 .404 .785 null null null 106 115 51 60 0 6758 243 6515 1.125 null null .889 null .17 null
2 1503 1039 115 119 1388 920 null null 124 130 null null null null null null null null 90 71 null null null null 1.509 .663 null null .753 null 52 332 .461 .722 null null null 105 114 67 76 0 2258 258 2000 1.441 null null .694 null .527 null
3 962 536 113 124 849 412 null null 120 139 null null null null null null null null 67 56 null null null null 2.061 .485 null null .686 null 52 339 .316 .691 null null null 106 115 83 92 0 1165 269 896 1.055 null null .948 null .078 null
4 4762 1980 115 142 4647 1838 null null 126 155 null null null null null null null null 94 94 null null null null 2.528 .396 null null .428 null 52 330 .257 .637 null null null 105 114 100 109 0 4304 308 3996 .86 null null 1.163 null -.218 null
5 4238 2934 111 149 4127 2785 null null 121 164 null null null null null null null null 95 82 null null null null 1.482 .675 null null .632 null 80 405 .466 .702 null null null 104 114 117 127 0 6378 323 6055 1.467 null null .682 null .553 null
6 1099 635 112 137 987 498 null null 121 157 null null null null null null null null 80 71 null null null null 1.982 .505 null null .618 null 52 272 .304 .629 null null null 104 113 132 141 0 1380 297 1083 1.097 null null .911 null .134 null
7 7914 4480 115 136 7799 4344 null null 126 150 null null null null null null null null 98 95 null null null null 1.795 .557 null null .545 null 156 779 .499 .867 null null null 101 116 145 160 0 9739 295 9444 1.211 null null .826 null .276 null
8 2121 1199 113 129 2008 1070 null null 121 142 null null null null null null null null 96 10 null null null null 1.877 .533 null null .561 null 52 309 .366 .657 null null null 103 112 165 174 0 2606 280 2326 1.158 null null .863 null .212 null
9 927 891 118 142 809 749 null null 127 160 null null null null null null null null 61 84 null null null null 1.08 .926 null null 1.231 null 52 321 .445 .628 null null null 104 113 180 189 0 1936 308 1628 2.012 null null .497 null 1.009 null
10 2589 1446 115 157 2474 1289 null null 124 168 null null null null null null null null 97 90 null null null null 1.919 .521 null null .542 null 80 372 .335 .675 null null null 103 114 197 208 0 3143 341 2802 1.133 null null .883 null .18 null
11 2995 1705 114 164 2881 1541 null null 123 178 null null null null null null null null 94 95 null null null null 1.87 .535 null null .487 null 156 575 .385 .716 null null null 102 116 211 225 0 3706 356 3350 1.163 null null .86 null .218 null
12 4077 4431 117 155 3960 4276 null null 126 170 null null null null null null null null 93 87 null null null null .926 1.08 null null 1.045 null 80 407 .836 .811 null null null 102 113 228 239 0 9632 336 9296 2.347 null null .426 null 1.231 null
13 844 836 128 179 716 657 null null 137 191 null null null null null null null null 90 84 null null null null 1.09 .918 null null .843 null 52 335 .568 .58 null null null 103 112 245 254 0 1817 389 1428 1.994 null null .501 null .996 null
14 1034 692 121 172 913 520 null null 131 187 null null null null null null null null 86 69 null null null null 1.756 .57 null null .724 null 52 333 .386 .682 null null null 104 113 261 270 0 1504 373 1131 1.239 null null .807 null .309 null
15 1385 883 119 160 1266 723 null null 126 183 null null null null null null null null 90 86 null null null null 1.751 .571 null null .534 null 52 353 .414 .746 null null null 103 112 277 286 0 1919 347 1572 1.242 null null .805 null .312 null
16 2376 1224 123 158 2253 1066 null null 131 169 null null null null null null null null 10 92 null null null null 2.114 .473 null null .483 null 52 342 .336 .706 null null null 103 112 294 303 -100 2660 343 2317 1.028 null null .972 null .04 null
17 4449 2182 128 164 4321 2018 null null 140 176 null null null null null null null null 95 86 null null null null 2.141 .467 null null .495 null 80 387 .336 .733 null null null 103 113 310 320 0 4743 356 4387 1.015 null null .985 null .022 null
18 2858 1455 128 169 2730 1286 null null 141 183 null null null null null null null null 10 90 null null null null 2.123 .471 null null .507 null 52 323 .315 .68 null null null 102 111 326 335 0 3163 367 2796 1.024 null null .976 null .034 null
19 3000 1323 128 207 2872 1116 null null 142 218 null null null null null null null null 88 71 null null null null 2.573 .389 null null .439 null 52 344 .341 .764 null null null 102 111 342 351 0 2876 450 2426 .845 null null 1.184 null -.243 null
20 6412 3417 128 210 6284 3207 null null 139 223 null null null null null null null null 92 85 null null null null 1.959 .51 null null .727 null 80 403 .369 .71 null null null 103 113 358 368 0 7428 456 6972 1.109 null null .901 null .15 null

Total number of rows: 21120

Table truncated, full table size 5126 Kbytes.




Supplementary data files not provided
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