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Sample GSM94440 Query DataSets for GSM94440
Status Public on Feb 01, 2006
Title "MA24-3(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 MA24-3(A) (red)
Organism Caenorhabditis elegans
Characteristics MA24-3(A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16500.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 1122 806 248 190 874 616 894 728 266 204 646 538 0 0 567 371 105 84 98 97 95 92 1490 1184 1.419 .705 .833 .827 .725 .525 156 939 .624 .9 150 2080 18860 82 97 48 63 0 657 155 502 .575 594 439 1.739 .679 -.799 -.558
2 620 486 249 191 371 295 384 254 266 205 135 63 0 0 483 416 99 81 58 46 41 41 666 198 1.258 .795 .467 1.054 .874 1.07 80 393 .674 .8 100 2250 18860 85 95 68 78 0 396 156 241 .649 207 51 1.542 .381 -.625 -1.393
3 321 286 241 181 80 105 267 230 261 196 26 49 0 0 165 188 114 91 34 34 15 19 185 75 .762 1.313 1.885 2.775 .775 6.722 52 267 .517 .52 80 2420 18870 87 95 86 94 0 233 148 86 1.071 188 40 .934 1.537 .099 .62
4 334 319 231 175 103 144 245 221 254 193 14 46 0 0 257 244 111 87 26 40 17 22 247 60 .715 1.398 3.286 2.138 .719 4.295 80 377 .656 .69 110 2590 18850 83 94 101 112 0 260 143 117 1.14 180 38 .877 2.68 .19 1.422
5 878 1103 231 174 647 929 794 940 246 186 563 766 0 0 566 834 97 71 76 83 71 77 1576 1329 .696 1.436 1.361 1.665 1.369 1.421 256 1224 1.336 .92 180 2740 18840 79 97 113 131 0 900 142 758 1.171 767 625 .854 1.11 .228 .15
6 559 500 234 185 325 315 349 286 257 196 115 101 0 0 490 413 109 76 50 52 40 47 640 216 1.032 .969 .878 3.565 1.027 11.294 80 359 .702 .81 100 2930 18850 84 94 136 146 0 408 151 257 .791 233 82 1.265 .716 -.339 -.481
7 293 214 240 186 53 28 271 203 256 195 31 17 0 0 109 74 99 66 25 15 10 11 81 48 1.893 .528 .548 1.634 .648 2.773 80 437 .213 .34 110 3080 18840 82 93 150 161 0 175 152 23 .431 166 14 2.32 .447 -1.214 -1.161
8 574 476 239 184 335 292 272 257 271 207 33 73 0 0 581 480 324 266 26 26 23 19 627 106 1.147 .872 2.212 1.844 .902 2.809 52 196 .698 .84 80 3250 18860 86 94 169 177 0 388 150 238 .711 210 60 1.406 1.805 -.492 .852
9 595 1492 241 194 354 1298 515 820 274 212 274 626 0 0 398 1585 228 183 50 71 34 59 1652 900 .273 3.667 2.285 5.005 2.985 10.024 120 466 2.18 .75 130 3400 18850 82 95 181 194 0 1217 158 1059 2.991 669 511 .334 1.864 1.581 .898
10 440 274 247 193 193 81 354 203 265 205 107 10 0 0 271 210 98 70 50 34 37 24 274 117 2.383 .42 .093 2.536 .562 9.222 156 514 .388 .54 140 3570 18870 84 98 198 212 0 224 157 66 .342 166 8 2.921 .076 -1.546 -3.713
11 540 358 239 188 301 170 428 268 253 200 189 80 0 0 349 223 97 70 64 52 50 39 471 269 1.771 .565 .423 2.059 .538 8.675 156 545 .496 .79 140 3730 18860 83 97 214 228 0 292 153 139 .461 219 65 2.171 .345 -1.118 -1.534
12 285 311 225 176 60 135 226 214 240 187 1 38 0 0 157 398 97 62 32 36 13 19 195 39 .444 2.25 38 2.803 .86 5.279 52 235 .738 .37 80 3870 18850 85 93 231 239 0 254 144 110 1.835 175 31 .545 30.998 .876 4.954
13 896 747 242 185 654 562 412 286 255 200 170 101 0 0 852 782 96 82 61 53 48 45 1216 271 1.164 .859 .594 2.752 .812 12.275 80 486 .85 .95 110 4060 18850 83 94 248 259 0 609 151 458 .701 233 82 1.427 .485 -.513 -1.045
14 423 509 241 180 182 329 265 273 253 195 24 93 0 0 441 619 102 76 30 52 21 35 511 117 .553 1.808 3.875 1.712 1.018 1.971 80 389 1.045 .75 100 4230 18840 83 93 266 276 0 415 147 268 1.475 223 76 .678 3.161 .56 1.66
15 551 396 228 176 323 220 394 271 253 197 166 95 0 0 404 276 177 124 48 48 33 41 543 261 1.468 .681 .572 2.451 .707 7.427 80 432 .548 .79 110 4380 18830 81 92 280 291 0 323 144 179 .556 221 77 1.8 .467 -.848 -1.099
16 562 554 221 179 341 375 361 294 235 191 140 115 0 0 431 477 94 71 57 57 46 48 716 255 .909 1.1 .821 1.238 .834 1.249 52 325 .939 .87 90 4530 18840 83 92 296 305 0 452 146 306 .897 240 94 1.115 .67 -.157 -.578
17 929 1823 222 181 707 1642 581 957 230 191 359 776 0 0 800 2039 81 68 73 80 61 70 2349 1135 .431 2.322 2.162 2.981 2.092 6.84 80 385 2.311 .94 110 4700 18830 81 92 312 323 0 1487 148 1339 1.895 781 633 .528 1.763 .922 .818
18 559 552 220 178 339 374 453 510 230 189 233 332 0 0 382 375 82 74 64 66 59 61 713 565 .906 1.103 1.425 1.478 1.118 1.719 208 765 .87 .86 160 4870 18820 78 94 327 343 0 450 145 305 .9 416 271 1.111 1.162 -.152 .217
19 290 255 219 180 71 75 254 184 231 193 35 4 0 0 198 250 85 75 23 18 11 13 146 39 .947 1.056 .114 4.364 .577 14.653 80 346 .591 .56 110 5040 18820 80 91 346 357 0 208 147 61 .862 150 3 1.16 .093 -.215 -3.423
20 231 199 221 181 10 18 221 177 232 189 0 -4 0 0 106 94 77 58 17 16 6 8 28 -4 .556 1.8 null 1.414 .541 2.409 80 390 .163 .22 110 5210 18810 79 90 363 374 0 162 148 15 1.468 144 -3 .681 null .554 null

Total number of rows: 21888

Table truncated, full table size 4769 Kbytes.




Supplementary data files not provided
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