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Sample GSM90746 Query DataSets for GSM90746
Status Public on Jan 06, 2006
Title EM673(lin-22) (red) vs. EM672(hlh-2; lin-32) (repeat #2) (green)
Sample type RNA
 
Channel 1
Source name EM672(hlh-2; lin-32) (green)
Organism Caenorhabditis elegans
Characteristics EM672(hlh-2; lin-32) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name EM673(lin-22) (red)
Organism Caenorhabditis elegans
Characteristics EM673(lin-22) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16835.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 05, 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)
GSE3979 Sensory ray genes

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
1 425 268 43 141 382 127 306 237 46 148 263 96 0 0 378 147 14 68 75 58 69 44 509 359 3.008 .332 .365 1.675 .388 5.637 120 479 .303 .73 120 2130 18510 73 85 67 79 0 306 161 145 .379 270 109 2.637 .416 -1.399 -1.264
2 273 268 52 146 221 122 246 244 56 156 194 98 0 0 156 133 21 66 91 62 84 39 343 292 1.811 .552 .505 1.146 .641 2.275 156 490 .534 .67 140 2290 18530 74 88 82 96 0 306 167 139 .63 278 112 1.588 .576 -.667 -.795
3 87 183 65 148 22 35 81 176 67 156 16 28 0 0 31 75 20 66 45 25 22 8 57 44 .629 1.591 1.75 2.935 2.063 3.119 80 367 .343 .12 110 2450 18520 74 85 99 110 0 209 169 40 1.815 201 32 .551 1.996 .86 .997
4 221 280 68 146 153 134 220 254 77 156 152 108 0 0 112 135 62 69 75 61 58 41 287 260 1.142 .876 .711 2.707 .894 6.623 80 487 .727 .62 110 2610 18500 72 83 115 126 0 319 167 153 .999 290 123 1.001 .81 -.001 -.303
5 890 439 54 147 836 292 988 394 66 157 934 247 0 0 748 315 58 70 73 67 68 58 1128 1181 2.863 .349 .264 .823 .384 1.197 120 590 .353 .88 130 2810 18510 72 85 134 147 0 501 168 333 .398 449 282 2.51 .302 -1.328 -1.729
6 68 166 53 146 15 20 63 154 58 156 10 8 0 0 28 73 22 70 27 22 11 6 35 18 .75 1.333 .8 6.161 2.455 7.708 80 384 .11 .03 110 2930 18520 74 85 147 158 0 189 167 23 1.521 176 9 .658 .912 .605 -.132
7 604 242 54 145 550 97 596 236 58 153 542 91 0 0 297 106 20 64 97 57 97 40 647 633 5.67 .176 .168 .255 .207 .205 120 579 .175 .56 130 3110 18500 71 84 164 177 0 276 165 111 .201 269 104 4.971 .192 -2.314 -2.385
8 161 195 70 145 91 50 149 195 82 150 79 50 0 0 72 78 42 60 70 46 45 22 141 129 1.82 .549 .633 4.09 .875 13.893 80 352 .296 .24 110 3260 18520 74 85 180 191 0 222 165 57 .627 222 57 1.596 .722 -.674 -.47
9 406 283 97 145 309 138 388 282 116 152 291 137 0 0 137 114 67 63 99 70 89 53 447 428 2.239 .447 .471 .523 .456 .386 120 439 .427 .62 120 3430 18510 73 85 197 209 0 323 165 157 .509 322 156 1.963 .537 -.973 -.897
10 306 232 127 143 179 89 293 217 133 152 166 74 0 0 75 93 67 68 95 52 68 30 268 240 2.011 .497 .446 .711 .588 .532 80 345 .36 .36 110 3580 18520 74 85 212 223 0 265 163 102 .567 248 84 1.763 .508 -.818 -.976
11 603 341 47 143 556 198 561 281 72 153 514 138 0 0 376 187 71 68 90 72 83 51 754 652 2.808 .356 .268 1.134 .377 5.869 156 627 .362 .8 150 3750 18510 71 86 227 242 0 389 163 226 .406 321 157 2.462 .306 -1.3 -1.707
12 124 191 43 144 81 47 113 189 50 153 70 45 0 0 51 66 68 66 53 33 16 7 128 115 1.723 .58 .643 1.502 .64 2.427 80 378 .191 .24 110 3900 18520 74 85 244 255 0 218 164 54 .662 216 51 1.511 .733 -.595 -.448
13 171 178 44 144 127 34 153 174 47 150 109 30 0 0 114 72 16 63 76 30 73 11 161 139 3.735 .268 .275 1.057 .417 1.804 52 233 .258 .32 80 4090 18520 76 84 265 273 0 203 164 39 .305 198 34 3.275 .314 -1.711 -1.671
14 96 212 43 148 53 64 78 202 46 152 35 54 0 0 54 74 14 64 76 42 55 23 117 89 .828 1.208 1.543 3.886 1.667 8.753 52 221 .733 .42 80 4210 18500 74 82 277 285 0 242 169 73 1.377 230 62 .726 1.76 .462 .815
15 83 192 43 144 40 48 75 172 45 150 32 28 0 0 37 90 13 62 72 35 60 15 88 60 .833 1.2 .875 4.526 2.081 6.415 80 444 .858 .32 110 4380 18530 75 86 292 303 0 219 164 55 1.369 196 32 .731 .998 .453 -.003
16 106 184 45 142 61 42 90 171 46 151 45 29 0 0 52 75 11 65 81 31 73 10 103 74 1.452 .689 .644 2.114 1.061 3.221 80 403 .549 .3 110 4540 18530 75 86 308 319 0 210 162 48 .785 195 33 1.273 .735 -.349 -.444
17 537 541 44 144 493 397 508 493 45 155 464 349 0 0 260 306 11 68 100 84 100 71 890 813 1.242 .805 .752 .857 .814 .634 120 494 .825 .88 130 4720 18520 73 86 325 338 0 617 164 453 .919 562 398 1.089 .858 -.123 -.221
18 104 206 45 143 59 63 91 184 46 151 46 41 0 0 55 98 12 65 81 42 61 20 122 87 .937 1.068 .891 2.476 1.358 3.352 120 422 .796 .4 120 4890 18520 74 86 343 355 0 235 163 72 1.218 210 47 .821 1.017 .284 .024
19 350 372 45 145 305 227 345 325 49 153 300 180 0 0 155 191 38 89 98 78 96 53 532 480 1.344 .744 .6 .862 .799 .483 80 366 .719 .77 110 5050 18530 75 86 359 370 0 424 165 259 .849 371 205 1.178 .684 -.236 -.547
20 447 358 45 145 402 213 449 348 46 153 404 203 0 0 182 158 11 61 100 82 100 64 615 607 1.887 .53 .502 .579 .537 .383 120 469 .517 .78 130 5210 18520 73 86 374 387 0 408 165 243 .604 397 232 1.655 .573 -.727 -.803

Total number of rows: 21504

Table truncated, full table size 4532 Kbytes.




Supplementary data files not provided
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