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Sample GSM69759 Query DataSets for GSM69759
Status Public on Aug 13, 2005
Title "mutant sorted touch cell (red, channel 2) vs. wt sorted touch cell (green, channel 1)"
Sample type RNA
 
Channel 1
Source name wt sorted touch cell (green)
Organism Caenorhabditis elegans
Characteristics wt sorted touch cell (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name mutant sorted touch cell (red)
Organism Caenorhabditis elegans
Characteristics mutant sorted touch cell (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17040.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 12, 2005
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)
GSE3121 Identification of genes expressed in C. elegans touch receptor neurons

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 358 226 138 152 220 74 374 226 146 154 236 74 0 0 93 58 45 41 90 71 88 43 294 310 2.973 .336 .314 .472 .384 .666 80 403 .311 .62 100 1240 16300 113 123 67 77 0 240 161 79 .357 240 79 2.801 .333 -1.486 -1.587
2 436 291 137 150 299 141 459 295 143 152 322 145 0 0 147 81 38 41 92 90 91 71 440 467 2.121 .472 .45 .719 .483 1.232 80 423 .407 .76 110 1400 16300 112 123 82 93 0 309 159 150 .5 313 154 1.998 .478 -.999 -1.065
3 312 214 133 145 179 69 328 215 138 149 195 70 0 0 127 64 33 39 81 66 76 40 248 265 2.594 .385 .359 .821 .395 1.818 80 394 .204 .59 100 1570 16300 113 123 100 110 0 227 154 73 .409 228 74 2.444 .381 -1.29 -1.392
4 298 246 135 147 163 99 306 231 143 150 171 84 0 0 112 79 47 40 76 72 67 51 262 255 1.646 .607 .491 1.03 .616 1.808 80 428 .407 .62 100 1740 16300 113 123 117 127 0 261 156 105 .645 245 89 1.551 .521 -.634 -.94
5 421 339 135 151 286 188 432 323 145 154 297 172 0 0 125 115 52 41 98 84 90 80 474 469 1.521 .657 .579 .74 .556 .617 52 334 .558 .74 90 1900 16300 113 122 133 142 0 360 160 200 .698 343 183 1.433 .615 -.52 -.702
6 231 211 135 157 96 54 210 215 141 161 75 58 0 0 88 53 38 44 63 59 50 23 150 133 1.778 .563 .773 1.436 .614 1.956 52 302 .281 .38 90 2060 16290 112 121 149 158 0 224 167 57 .597 228 62 1.675 .821 -.744 -.285
7 497 261 130 155 367 106 548 258 136 159 418 103 0 0 201 74 40 44 86 80 85 56 473 521 3.462 .289 .246 1.232 .295 5.489 120 487 .24 .67 120 2220 16290 111 123 164 176 0 277 164 112 .307 274 109 3.262 .262 -1.706 -1.935
8 373 241 129 152 244 89 376 241 133 157 247 89 0 0 101 55 29 43 98 81 95 55 333 336 2.742 .365 .36 .432 .392 .277 80 409 .277 .56 110 2380 16290 111 122 180 191 0 256 161 94 .387 256 94 2.583 .382 -1.369 -1.387
9 356 280 136 156 220 124 374 294 146 160 238 138 0 0 134 86 66 42 80 79 69 69 344 376 1.774 .564 .58 .811 .632 .741 120 510 .428 .73 120 2550 16290 111 123 197 209 0 297 166 132 .598 312 146 1.672 .615 -.741 -.701
10 597 322 139 158 458 164 505 309 151 160 366 151 0 0 413 89 74 43 96 91 92 81 622 517 2.793 .358 .413 .516 .423 .433 80 352 .188 .6 110 2710 16300 112 123 213 224 0 342 168 174 .38 328 160 2.632 .438 -1.396 -1.192
11 366 260 137 154 229 106 399 264 145 157 262 110 0 0 125 81 61 41 88 77 77 59 335 372 2.16 .463 .42 .989 .502 2.471 120 441 .249 .58 120 2860 16290 111 123 228 240 0 276 163 112 .491 280 117 2.036 .446 -1.026 -1.166
12 316 245 131 155 185 90 331 250 149 158 200 95 0 0 135 82 91 45 67 65 52 53 275 295 2.056 .486 .475 1.015 .506 2.358 120 475 .378 .66 120 3030 16290 111 123 245 257 0 260 164 96 .516 265 101 1.937 .504 -.954 -.988
13 302 266 132 152 170 114 295 242 136 155 163 90 0 0 100 95 37 40 88 84 78 55 284 253 1.491 .671 .552 .929 .748 .711 52 282 .525 .65 90 3180 16300 113 122 261 270 0 282 161 121 .712 257 96 1.405 .586 -.491 -.771
14 325 232 130 151 195 81 339 216 132 152 209 65 0 0 112 69 28 40 90 68 85 38 276 274 2.407 .415 .311 .595 .39 .747 80 387 .37 .67 100 3340 16290 112 122 277 287 0 246 160 86 .441 229 69 2.268 .33 -1.182 -1.599
15 283 204 129 153 154 51 286 198 132 156 157 45 0 0 103 61 29 39 86 58 80 32 205 202 3.02 .331 .287 1.132 .376 4.441 80 423 .285 .51 100 3500 16290 112 122 293 303 0 216 162 54 .351 210 48 2.845 .304 -1.509 -1.717
16 361 281 132 151 229 130 378 277 141 156 246 126 0 0 97 76 63 44 94 84 84 65 359 372 1.762 .568 .512 .743 .609 .649 52 352 .426 .64 90 3670 16280 111 120 310 319 0 298 160 138 .602 294 134 1.66 .544 -.731 -.879
17 466 507 132 151 334 356 485 500 140 155 353 349 0 0 223 228 57 43 83 88 73 83 690 702 .938 1.066 .989 1.25 1.03 .815 80 433 .886 .86 110 3830 16290 111 122 325 336 0 538 160 378 1.131 531 370 .884 1.049 .178 .069
18 410 384 130 150 280 234 447 391 135 155 317 241 0 0 145 141 28 40 93 91 88 85 514 558 1.197 .836 .76 1.281 .843 2.726 80 394 .779 .86 110 3990 16280 110 121 341 352 0 408 159 248 .887 415 256 1.128 .807 -.173 -.31
19 318 301 129 155 189 146 340 291 135 159 211 136 0 0 115 98 36 42 87 86 75 70 335 347 1.295 .772 .645 1.378 .828 2.842 120 536 .657 .79 130 4130 16280 109 122 354 367 0 319 164 155 .82 309 144 1.22 .684 -.287 -.548
20 334 264 128 157 206 107 328 269 133 161 200 112 0 0 142 85 34 40 85 76 77 60 313 312 1.925 .519 .56 1.004 .529 3.032 120 490 .468 .77 120 4300 16280 110 122 372 384 0 280 167 114 .551 285 119 1.814 .594 -.859 -.751

Total number of rows: 21504

Table truncated, full table size 4567 Kbytes.




Supplementary data files not provided
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