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Sample GSM94466 Query DataSets for GSM94466
Status Public on Feb 01, 2006
Title "PB306-4(A) (red, channel 2) vs. PB303-4(B) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name PB303-4(B) (green)
Organism Caenorhabditis elegans
Characteristics PB303-4(B) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PB306-4(A) (red)
Organism Caenorhabditis elegans
Characteristics PB306-4(A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17477.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
1 731 388 95 149 636 239 434 298 98 151 339 149 0 0 661 213 25 37 88 83 85 75 875 488 2.661 .376 .44 .736 .427 .821 80 454 .297 .85 110 2290 19670 65 76 71 82 0 313 120 193 .303 240 120 3.298 .355 -1.722 -1.496
2 92 128 84 120 8 8 84 121 88 125 0 1 0 0 39 40 27 32 11 17 8 3 16 1 1 1 null 2.744 1.324 4.164 80 374 .353 .36 110 2450 19680 66 77 87 98 0 103 97 6 .807 98 1 1.24 null -.31 null
3 103 109 83 115 20 -6 96 104 84 119 13 -11 0 0 28 29 25 25 37 13 13 3 14 2 null null null 2.349 .982 3.11 80 354 .233 .21 110 2610 19680 66 77 103 114 0 88 93 -5 null 84 -9 null null null null
4 804 400 75 99 729 301 467 269 79 100 392 170 0 0 810 317 26 36 80 79 70 68 1030 562 2.422 .413 .434 1.045 .515 1.373 120 409 .367 .92 120 2770 19680 66 78 119 131 0 323 80 243 .333 217 137 3.002 .35 -1.586 -1.515
5 942 335 74 94 868 241 932 316 78 94 858 222 0 0 796 206 25 30 77 78 70 68 1109 1080 3.602 .278 .259 .976 .303 2.62 120 537 .248 .92 130 2940 19680 65 78 135 148 0 270 76 194 .224 255 179 4.464 .209 -2.158 -2.26
6 112 121 78 104 34 17 92 107 92 115 14 3 0 0 60 55 117 127 9 3 1 1 51 17 2 .5 .214 4.496 1.375 14.564 52 257 .971 .92 90 3090 19700 69 78 152 161 0 98 84 14 .403 86 2 2.479 .173 -1.31 -2.532
7 360 234 81 106 279 128 338 198 89 113 257 92 0 0 218 115 81 88 73 51 62 32 407 349 2.18 .459 .358 .832 .459 1.499 156 644 .532 .81 150 3260 19680 64 79 166 181 0 189 86 103 .37 160 74 2.702 .289 -1.434 -1.792
8 194 192 81 109 113 83 167 158 88 110 86 49 0 0 103 98 64 23 57 60 37 50 196 135 1.361 .735 .57 1.439 .884 2.525 120 362 .549 .68 130 3430 19680 65 78 184 197 0 155 88 67 .593 127 40 1.688 .46 -.755 -1.121
9 4280 1333 78 104 4202 1229 2458 715 83 108 2380 611 0 0 4449 1362 47 40 69 72 66 68 5431 2991 3.419 .292 .257 1.441 .307 5.33 208 766 .287 .95 170 3600 19680 63 80 199 216 0 1075 84 992 .236 577 493 4.238 .207 -2.083 -2.271
10 156 159 74 101 82 58 148 135 77 102 74 34 0 0 65 71 20 25 80 52 70 42 140 108 1.414 .707 .459 1.179 .822 1.389 120 336 .64 .69 130 3760 19670 64 77 217 230 0 128 81 47 .571 109 27 1.752 .371 -.809 -1.432
11 1069 563 73 95 996 468 1081 470 77 96 1008 375 0 0 796 387 20 19 85 91 79 82 1464 1383 2.128 .47 .372 1.119 .488 2.634 156 501 .439 .92 150 3910 19680 64 79 231 246 0 454 77 378 .379 379 303 2.638 .3 -1.399 -1.736
12 137 167 75 98 62 69 132 157 78 100 57 59 0 0 48 58 18 21 78 76 62 60 131 116 .899 1.113 1.035 2.357 1.065 5.446 120 400 .792 .68 130 4070 19670 64 77 248 261 0 135 79 56 .898 127 48 1.114 .835 -.155 -.26
13 188 171 77 104 111 67 114 160 79 104 37 56 0 0 190 69 20 21 65 75 47 65 178 93 1.657 .604 1.514 2.124 1 2.811 120 426 .294 .68 130 4230 19670 64 77 264 277 0 138 84 54 .487 129 45 2.054 1.221 -1.038 .288
14 156 196 77 104 79 92 132 155 80 106 55 51 0 0 88 99 23 23 62 65 52 53 171 106 .859 1.165 .927 1.647 1.177 2.624 120 410 .948 .82 120 4390 19670 65 77 281 293 0 158 84 74 .94 125 41 1.064 .748 -.09 -.419
15 121 143 78 102 43 41 106 117 84 103 28 15 0 0 54 74 49 22 30 44 13 31 84 43 1.049 .953 .536 1.793 1.087 2.639 120 426 .714 .61 120 4550 19680 66 78 297 309 0 115 82 33 .769 94 12 1.3 .432 -.378 -1.21
16 223 243 76 98 147 145 210 189 78 100 134 91 0 0 119 147 19 19 85 80 78 67 292 225 1.014 .986 .679 1.201 .856 1.85 80 350 .909 .83 110 4710 19670 65 76 313 324 0 196 79 117 .796 152 73 1.257 .548 -.33 -.868
17 2061 1157 73 94 1988 1063 1705 985 76 95 1632 891 0 0 1765 988 20 20 88 91 83 81 3051 2523 1.87 .535 .546 1.022 .545 2.636 156 523 .513 .94 140 4880 19680 65 79 329 343 0 933 76 858 .431 795 719 2.318 .44 -1.213 -1.183
18 171 247 74 95 97 152 158 194 76 96 84 99 0 0 79 134 20 20 81 86 76 75 249 183 .638 1.567 1.179 1.85 1.508 2.04 80 324 1.326 .82 110 5040 19660 64 75 346 357 0 199 77 123 1.264 157 80 .791 .951 .338 -.073
19 586 379 76 97 510 282 283 173 79 98 207 76 0 0 582 366 21 18 78 70 70 58 792 283 1.809 .553 .367 .969 .585 1.711 120 341 .544 .9 120 5210 19680 66 78 363 375 0 306 78 228 .446 140 61 2.242 .296 -1.165 -1.755
20 1507 785 77 99 1430 686 925 380 80 99 848 281 0 0 1576 787 25 18 74 78 68 69 2116 1129 2.085 .48 .331 1.434 .529 4.463 208 692 .457 .93 160 5370 19670 63 79 377 393 0 633 80 553 .387 307 227 2.584 .267 -1.37 -1.903

Total number of rows: 21504

Table truncated, full table size 4563 Kbytes.




Supplementary data files not provided
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