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Sample GSM95248 Query DataSets for GSM95248
Status Public on Feb 03, 2006
Title N2 (green, channel 1) vs daf-8 (red, channel 2) Trial #2
Sample type RNA
 
Channel 1
Source name N2 (green, channel 1)
Organism Caenorhabditis elegans
Characteristics N2 (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name daf-8 (red, channel 2)
Organism Caenorhabditis elegans
Characteristics daf-8 (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15549.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 Feb 02, 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 GPL2754
Series (1)
GSE4164 Regulation of signaling genes by TGFbeta during entry into dauer diapause in C. 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 11972 16688 170 337 11802 16351 7193 3366 204 354 7023 3029 0 6 9417 22247 171 155 100 100 100 100 28153 10052 .722 1.385 .431 .629 .489 2.201 120 659 1.997 .92 120 1340 18690 43 55 24 36 0 20157 407 19750 1.673 4066 3659 .598 .521 .743 -.941
2 3917 4671 193 359 3724 4312 4022 3943 241 385 3829 3584 0 0 845 2602 218 185 100 100 100 100 8036 7413 .864 1.158 .936 .966 .925 1.671 52 374 1.419 .87 90 1510 18710 46 55 42 51 0 5642 434 5208 1.399 4763 4329 .715 1.131 .484 .177
3 569 845 207 349 362 496 561 808 228 364 354 459 0 0 160 194 103 120 100 100 83 91 858 813 .73 1.37 1.297 1.397 1.263 1.447 12 62 1.964 .73 40 1680 18700 48 52 62 66 0 1021 422 599 1.655 976 554 .604 1.566 .727 .647
4 4377 2697 179 348 4198 2349 4996 2449 203 358 4817 2101 0 0 2009 1872 103 105 100 96 100 96 6547 6918 1.787 .56 .436 .444 .435 2.049 52 358 .602 .86 90 1850 18690 44 53 76 85 0 3258 420 2837 .676 2958 2538 1.48 .527 -.565 -.925
5 10558 35057 176 327 10382 34730 13970 35046 188 336 13794 34719 0 28 6751 26061 73 97 100 100 100 100 45112 48513 .299 3.345 2.517 2.685 3.193 2.073 80 432 3.639 .97 100 2000 18680 43 53 91 101 0 42344 395 41949 4.041 42331 41936 .247 3.04 2.015 1.604
6 1098 1566 181 312 917 1254 1005 1386 194 320 824 1074 0 0 397 558 79 92 100 100 100 100 2171 1898 .731 1.368 1.303 1.377 1.437 1.545 12 87 1.339 .9 50 2180 18680 45 50 111 116 0 1892 377 1515 1.652 1674 1297 .605 1.574 .724 .655
7 16014 23679 166 325 15848 23354 19857 16448 193 370 19691 16123 0 3 8430 20901 170 422 99 100 99 98 39202 35814 .679 1.474 .819 .965 1.05 2.017 120 558 1.924 .9 120 2310 18700 44 56 121 133 0 28601 393 28209 1.78 19867 19475 .562 .989 .832 -.016
8 422 555 175 323 247 232 325 471 185 338 150 148 0 0 239 367 77 109 71 53 48 42 479 298 1.065 .939 .987 .986 .915 2.44 52 271 2.085 .75 80 2460 18690 45 53 138 146 -50 670 390 280 1.135 569 179 .881 1.192 .182 .253
9 1435 1166 190 345 1245 821 1432 1110 219 376 1242 765 0 0 214 393 121 201 100 100 100 86 2066 2007 1.516 .659 .616 .6 .599 1.525 52 318 .699 .84 80 2650 18690 45 53 157 165 0 1408 417 992 .797 1341 924 1.255 .744 -.328 -.427
10 948 716 190 364 758 352 952 655 227 393 762 291 0 0 152 276 128 213 100 69 100 28 1110 1053 2.153 .464 .382 .383 .39 2.074 52 274 .603 .69 80 2810 18690 45 53 173 181 0 865 440 425 .561 791 351 1.783 .461 -.834 -1.116
11 15198 14206 179 346 15019 13860 18798 14647 204 360 18619 14301 0 0 7658 10790 102 137 100 100 100 100 28879 32920 1.084 .923 .768 .708 .781 1.675 80 515 1.032 .93 110 2960 18670 41 52 186 197 0 17159 418 16741 1.115 17692 17274 .897 .928 .157 -.108
12 755 770 174 327 581 443 766 667 197 345 592 340 0 0 211 406 92 111 98 92 98 75 1024 932 1.312 .762 .574 .618 .633 2.032 52 299 1.1 .7 80 3140 18680 44 52 206 214 0 930 395 535 .921 806 411 1.086 .694 -.119 -.528
13 369 557 172 315 197 242 283 548 184 329 111 233 0 0 408 138 76 104 57 84 36 55 439 344 .814 1.228 2.099 1.797 1.724 2.826 52 305 .424 .41 80 3290 18690 45 53 221 229 0 673 380 292 1.484 662 281 .674 2.535 .569 1.342
14 471 558 151 324 320 234 452 546 171 327 301 222 0 0 119 157 81 99 100 78 93 50 554 523 1.368 .731 .738 .643 .661 1.974 32 236 1.075 .7 70 3460 18680 44 51 238 245 0 674 391 283 .883 659 268 1.132 .891 -.179 -.167
15 652 637 145 313 507 324 653 594 155 326 508 281 0 0 112 187 69 93 100 100 100 84 831 789 1.565 .639 .553 .571 .545 1.572 32 227 .728 .72 70 3620 18690 45 52 254 261 0 769 378 391 .772 717 339 1.296 .668 -.374 -.582
16 1019 913 142 305 877 608 1055 875 159 315 913 570 0 0 220 259 89 87 100 100 98 96 1485 1483 1.442 .693 .624 .66 .689 1.546 52 281 .736 .88 80 3780 18680 44 52 270 278 0 1103 368 734 .837 1057 688 1.194 .754 -.256 -.407
17 12143 3912 147 311 11996 3601 12501 3980 166 317 12354 3669 0 0 6646 2238 96 92 100 96 100 93 15597 16023 3.331 .3 .297 .271 .3 1.954 80 420 .301 .97 100 3930 18670 42 52 284 294 0 4725 376 4350 .363 4807 4432 2.758 .359 -1.464 -1.479
18 936 845 149 324 787 521 915 836 164 329 766 512 0 0 224 236 74 91 100 98 100 96 1308 1278 1.511 .662 .668 .612 .648 1.686 52 300 .688 .84 80 4090 18680 44 52 301 309 0 1021 391 629 .8 1010 618 1.251 .807 -.323 -.309
19 5613 4002 146 320 5467 3682 5836 4144 166 325 5690 3824 0 0 1472 1279 79 92 100 100 100 100 9149 9514 1.485 .673 .672 .643 .675 1.372 52 345 .67 .96 90 4250 18680 43 52 316 325 0 4834 387 4447 .813 5005 4619 1.229 .812 -.298 -.301
20 1404 597 144 311 1260 286 1558 588 162 323 1414 277 0 0 437 201 71 96 100 81 98 63 1546 1691 4.406 .227 .196 .19 .223 2.071 80 407 .242 .77 100 4420 18670 42 52 333 343 0 721 376 345 .274 710 335 3.647 .237 -1.867 -2.079

Total number of rows: 21504

Table truncated, full table size 4826 Kbytes.




Supplementary data files not provided

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