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Sample GSM94446 Query DataSets for GSM94446
Status Public on Feb 01, 2006
Title PB303-3(A) (red, channel 2) vs. N2-3(B) (green, channel 1)
Sample type RNA
 
Channel 1
Source name N2-3(B) (green)
Organism Caenorhabditis elegans
Characteristics N2-3(B) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PB303-3(A) (red)
Organism Caenorhabditis elegans
Characteristics PB303-3(A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17416.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 GPL3178
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 1086 385 58 140 1028 245 645 243 80 183 587 103 0 0 1172 383 327 575 64 15 45 5 1273 690 4.196 .238 .175 1.558 .241 5.133 208 1237 .557 .67 170 1440 18250 104 121 71 88 0 533 194 339 .33 336 142 3.033 .243 -1.601 -2.043
2 100 172 59 154 41 18 63 160 64 157 4 6 0 0 91 77 34 56 26 30 17 7 59 10 2.278 .439 1.5 9.721 1.688 18.414 80 368 .261 .32 110 1580 18250 107 118 88 99 0 238 213 25 .607 221 8 1.647 2.075 -.719 1.053
3 60 151 59 150 1 1 56 147 66 153 -3 -3 0 0 16 50 51 57 1 13 0 2 2 -6 1 1 null 5.578 3.648 5.311 80 438 -1 -1 110 1740 18250 107 118 104 115 0 209 208 1 1.383 203 -4 .723 null .468 null
4 325 229 61 148 264 81 65 136 67 153 4 -12 0 0 1269 400 39 55 16 15 13 11 345 -8 3.259 .307 null 5.161 2.093 10.363 80 458 .412 .92 110 1910 18250 107 118 121 132 0 317 205 112 .424 188 -17 2.356 null -1.236 null
5 1271 552 68 169 1203 383 976 352 75 175 908 183 0 0 1267 557 40 77 70 61 66 53 1586 1091 3.141 .318 .202 1.683 .345 5.486 156 658 .334 .83 150 2100 18260 106 121 138 153 0 764 234 530 .44 487 253 2.271 .279 -1.183 -1.843
6 468 311 70 180 398 131 387 286 71 185 317 106 0 0 340 147 23 69 94 59 89 41 529 423 3.038 .329 .334 .75 .4 2.069 120 391 .326 .74 120 2270 18270 109 121 157 169 0 430 249 181 .455 396 147 2.196 .463 -1.135 -1.112
7 77 197 72 193 5 4 74 177 76 195 2 -16 0 0 26 88 27 71 18 18 5 7 9 -14 1.25 .8 null 4.19 2.652 4.611 80 382 .571 .22 110 2390 18250 107 118 169 180 0 273 267 6 1.107 245 -22 .904 null .146 null
8 69 181 67 179 2 2 64 166 72 186 -3 -13 0 0 29 79 27 68 11 17 3 5 4 -16 1 1 null 6.615 3.75 10.452 80 527 .101 .04 110 2550 18260 108 119 185 196 0 250 248 3 1.383 230 -18 .723 null .468 null
9 2803 848 59 161 2744 687 543 305 64 167 484 144 0 0 3871 978 23 61 78 65 76 55 3431 628 3.994 .25 .298 1.336 .337 4.196 52 379 .234 .92 90 2750 18260 109 118 206 215 0 1173 223 950 .346 422 199 2.887 .412 -1.53 -1.281
10 202 221 54 156 148 65 129 173 58 162 75 17 0 0 161 107 22 60 75 36 65 26 213 92 2.277 .439 .227 4.886 .49 11.256 52 248 .44 .6 80 2920 18260 110 118 224 232 0 306 216 90 .608 239 24 1.646 .314 -.719 -1.673
11 2149 1822 58 166 2091 1656 2787 1670 307 334 2729 1504 0 0 1667 1591 775 732 63 61 62 50 3747 4233 1.263 .792 .551 1.481 .729 2.036 80 428 .925 .85 110 3040 18260 108 119 234 245 0 2521 230 2291 1.096 2310 2081 .913 .762 .132 -.391
12 132 180 54 165 78 15 59 156 275 316 5 -9 0 0 306 127 734 691 3 0 2 0 93 -4 5.2 .192 null 6.509 2.417 9.77 80 483 .866 .89 110 3200 18260 108 119 250 261 0 249 228 21 .266 216 -12 3.759 null -1.91 null
13 57 161 50 154 7 7 49 158 53 157 -1 4 0 0 42 52 17 62 15 16 5 0 14 3 1 1 null 12.347 6.632 18.266 80 450 -1 -1 110 3370 18260 108 119 267 278 0 223 213 10 1.383 219 6 .723 null .468 null
14 54 151 51 148 3 3 51 148 55 152 0 0 0 0 17 50 20 57 13 16 5 0 6 0 1 1 null 4.822 2.545 6.764 80 436 .198 .08 110 3530 18260 108 119 283 294 0 209 205 4 1.383 205 0 .723 null .468 null
15 63 174 51 144 12 30 52 158 57 155 1 14 0 0 40 98 30 63 13 15 5 11 42 15 .4 2.5 14 8.941 3.684 14.654 80 444 1.114 .43 110 3690 18260 108 119 299 310 0 241 199 42 3.458 219 19 .289 19.367 1.79 4.276
16 1119 713 52 153 1067 560 866 427 122 256 814 274 0 0 1095 744 786 1033 50 17 30 8 1627 1088 1.905 .525 .337 1.534 .555 2.873 156 627 .564 .9 140 3880 18260 107 121 317 331 0 986 212 775 .726 591 379 1.377 .466 -.462 -1.103
17 1014 544 49 149 965 395 466 293 52 154 417 144 0 0 1120 547 24 61 70 65 63 53 1360 561 2.443 .409 .345 1.833 .414 8.661 120 427 .414 .89 120 4040 18270 109 121 334 346 0 753 206 546 .566 405 199 1.766 .478 -.82 -1.066
18 185 228 47 138 138 90 69 200 50 145 22 62 0 0 175 124 16 63 61 46 44 34 228 84 1.533 .652 2.818 3.98 .968 6.638 52 273 .546 .63 90 4210 18280 111 120 352 361 0 315 191 125 .902 277 86 1.108 3.899 -.148 1.963
19 54 147 49 142 5 5 49 137 51 148 0 -5 0 0 25 61 16 69 17 13 7 6 10 -5 1 1 null 8.647 3.777 17.242 80 394 .993 .26 110 4340 18260 108 119 364 375 0 203 196 7 1.383 190 -7 .723 null .468 null
20 112 254 52 148 60 106 55 156 55 156 3 8 0 0 247 408 28 70 16 20 8 11 166 11 .566 1.767 2.667 6.698 2.32 10.031 80 385 1.178 .7 110 4500 18260 108 119 380 391 0 351 205 147 2.444 216 11 .409 3.689 1.289 1.883

Total number of rows: 21888

Table truncated, full table size 4669 Kbytes.




Supplementary data files not provided
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