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Sample GSM94472 Query DataSets for GSM94472
Status Public on Feb 01, 2006
Title "PB306-2(B) (red, channel 2) vs. AB1-2(A) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name AB1-2(A) (green)
Organism Caenorhabditis elegans
Characteristics AB1-2(A) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PB306-2(B) (red)
Organism Caenorhabditis elegans
Characteristics PB306-2(B) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17479.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 GPL2646
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
1 191 84 35 44 156 40 121 69 36 46 86 25 0 0 165 48 9 14 80 58 68 47 196 111 3.9 .256 .291 1.183 .294 4.352 80 455 .234 .79 110 2400 19490 91 102 38 49 0 64 33 30 .194 52 19 5.141 .221 -2.362 -2.181
2 48 49 36 45 12 4 39 44 40 48 3 -1 0 0 58 22 28 14 8 16 1 6 16 2 3 .333 null 2.388 1.417 2.996 80 383 .183 .41 110 2590 19500 92 103 57 68 0 37 34 3 .253 33 -1 3.955 null -1.984 null
3 71 65 37 46 34 19 59 58 41 49 22 12 0 0 52 22 28 15 42 38 15 26 53 34 1.789 .559 .545 .949 .733 .856 52 276 .249 .39 90 2730 19480 91 100 72 81 0 49 35 14 .424 44 9 2.359 .414 -1.238 -1.273
4 158 162 36 46 122 116 123 112 40 49 87 66 0 0 131 130 14 17 70 73 61 63 238 153 1.052 .951 .759 1.7 1.079 1.99 120 396 .836 .86 120 2910 19490 91 103 89 101 0 123 35 88 .721 85 50 1.387 .575 -.471 -.797
5 132 257 37 50 95 207 102 200 41 51 65 150 0 0 104 243 20 16 62 75 59 69 302 215 .459 2.179 2.308 3.048 2 4.666 120 388 2.728 .52 120 3070 19490 91 103 105 117 0 195 38 157 1.653 152 114 .605 1.75 .725 .808
6 60 67 40 51 20 16 51 59 44 53 11 8 0 0 40 31 19 18 30 30 11 13 36 19 1.25 .8 .727 2.046 1.023 4.223 80 382 .345 .63 110 3230 19500 92 103 121 132 0 51 39 12 .607 45 6 1.648 .552 -.721 -.858
7 213 194 42 55 171 139 208 180 93 108 166 125 0 0 130 125 440 585 0 0 0 0 310 291 1.23 .813 .753 1.073 .766 1.041 120 507 .689 .85 130 3400 19480 89 102 137 150 0 147 42 105 .617 137 95 1.622 .571 -.698 -.808
8 122 143 43 59 79 84 97 134 116 240 54 75 0 0 163 86 505 1090 1 0 0 0 163 129 .94 1.063 1.389 2.67 1.261 5.713 120 392 .502 .64 130 3570 19480 89 102 154 167 0 108 45 64 .807 102 57 1.24 1.054 -.31 .075
9 1126 1121 42 55 1084 1066 695 268 108 184 653 213 0 0 1158 1342 688 977 49 37 34 25 2150 866 1.017 .983 .326 1.445 .926 2.823 208 786 .806 .72 170 3720 19480 87 104 167 184 0 850 42 809 .746 203 162 1.341 .247 -.423 -2.015
10 85 137 43 57 42 80 75 95 142 226 32 38 0 0 46 96 998 1246 0 0 0 0 122 70 .525 1.905 1.188 2.616 1.873 3.017 120 280 1.279 .76 120 3890 19480 90 102 187 199 0 104 43 61 1.445 72 29 .692 .901 .531 -.151
11 265 720 42 60 223 660 213 463 104 133 171 403 0 0 211 698 629 450 5 46 0 33 883 574 .338 2.96 2.357 3.835 2.723 6.753 156 427 2.632 .84 140 4040 19480 89 103 201 215 0 546 46 501 2.245 351 306 .445 1.788 1.167 .838
12 110 197 41 60 69 137 107 171 70 109 66 111 0 0 57 129 196 297 1 11 0 0 206 177 .504 1.986 1.682 2.392 1.906 1.824 120 436 1.072 .58 130 4200 19480 89 102 217 230 0 149 46 104 1.506 130 84 .664 1.276 .591 .351
13 634 1437 41 70 593 1367 48 138 57 92 7 68 0 0 3385 5824 71 85 26 44 15 32 1960 75 .434 2.305 9.714 10.991 4.467 15.205 52 186 .477 .28 80 4360 19430 87 95 236 244 0 1090 53 1037 1.749 105 52 .572 7.369 .806 2.881
14 96 148 39 58 57 90 84 113 87 100 45 55 0 0 53 98 802 338 0 0 0 0 147 100 .633 1.579 1.222 3.076 1.614 7.627 120 481 1.252 .74 120 4540 19470 89 101 252 264 0 112 44 68 1.198 86 42 .835 .927 .26 -.109
15 92 136 38 49 54 87 85 97 43 63 47 48 0 0 45 99 47 93 48 33 15 16 141 95 .621 1.611 1.021 2.081 1.472 2.103 80 383 1.24 .65 110 4690 19480 90 101 267 278 0 103 37 66 1.222 74 36 .818 .775 .289 -.368
16 96 142 38 49 58 93 83 82 41 52 45 33 0 0 67 118 15 20 60 61 52 47 151 78 .624 1.603 .733 2.968 1.511 5.481 120 382 1.437 .84 120 4860 19480 90 102 284 296 0 108 37 71 1.216 62 25 .822 .556 .282 -.846
17 495 881 39 49 456 832 281 344 55 71 242 295 0 0 463 924 163 142 55 56 46 50 1288 537 .548 1.825 1.219 2.197 1.664 2.575 156 532 1.812 .94 150 5020 19480 88 103 298 313 0 668 37 631 1.384 261 224 .723 .925 .469 -.113
18 100 173 40 48 60 125 82 138 40 50 42 90 0 0 56 125 9 15 76 75 67 71 185 132 .48 2.083 2.143 2.771 2 2.948 80 327 1.817 .86 110 5180 19460 88 99 316 327 0 131 36 95 1.58 105 68 .633 1.625 .66 .701
19 205 266 39 50 166 216 152 178 40 52 113 128 0 0 153 217 10 15 83 80 78 75 382 241 .769 1.301 1.133 1.905 1.265 2.242 120 432 1.214 .89 130 5340 19480 89 102 331 344 0 202 38 164 .987 135 97 1.013 .859 -.019 -.219
20 520 782 38 51 482 731 440 543 40 53 402 492 0 0 378 713 9 15 88 89 83 83 1213 894 .659 1.517 1.224 1.594 1.454 1.309 156 579 1.595 .94 150 5510 19480 88 103 347 362 0 593 39 554 1.15 412 373 .869 .928 .202 -.107

Total number of rows: 21504

Table truncated, full table size 4409 Kbytes.




Supplementary data files not provided
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