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Sample GSM75935 Query DataSets for GSM75935
Status Public on Sep 24, 2005
Title DES genomic DNA vs. MHY26 (dun1) genomic DNA (correct version)
Sample type genomic
 
Channel 1
Source name DES460 (wt) genomic DNA
Organism Saccharomyces cerevisiae
Characteristics DES460 (wt) genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name MHY1 (dun1) genomic DNA
Organism Saccharomyces cerevisiae
Characteristics MHY1 (dun1) genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Yeast expression, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16514.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 Sep 23, 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 GPL2870
Series (1)
GSE3358 DNA damage responses and Mec1p

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 12659 13247 1757 497 10902 12750 13656 14361 1786 549 11899 13864 0 0 3290 3579 446 326 100 100 98 100 23652 25763 .855 1.17 1.165 1.341 1.182 .795 120 812 1.095 .94 130 3280 13430 316 329 117 130 0 16269 610 15659 1.436 17638 17027 .696 1.431 .522 .517
2 21018 20640 1760 514 19258 20126 22303 21486 1786 554 20543 20972 0 0 7705 6814 443 202 100 100 99 100 39384 41515 .957 1.045 1.021 1.306 1.025 1.228 120 666 .929 .93 120 3490 13440 318 330 139 151 0 25349 631 24718 1.284 26388 25757 .779 1.254 .36 .326
3 13043 13577 1739 499 11304 13078 13458 13584 1779 540 11719 13085 0 0 5686 5914 480 243 100 100 100 100 24382 24804 .864 1.157 1.117 1.496 1.132 1.665 120 775 1.035 .92 130 3710 13440 317 330 160 173 0 16675 613 16062 1.421 16683 16070 .704 1.371 .507 .456
4 13462 13725 1798 482 11664 13243 14857 15558 1858 603 13059 15076 0 0 3726 4385 563 513 98 100 97 100 24907 28135 .881 1.135 1.154 1.413 1.151 2.735 156 938 1.079 .94 150 3930 13430 315 330 181 196 0 16857 592 16265 1.394 19108 18516 .717 1.418 .48 .504
5 5439 3886 1790 476 3649 3410 5503 3953 1881 567 3713 3477 0 0 1308 1208 629 367 96 100 95 98 7059 7190 1.07 .935 .936 .975 .977 .352 120 723 .831 .88 130 4140 13440 317 330 203 216 0 4773 585 4188 1.148 4855 4270 .871 1.15 .199 .202
6 8343 7239 1721 494 6622 6745 8560 7222 1976 661 6839 6728 0 0 1963 2027 2666 1267 94 97 81 96 13367 13567 .982 1.019 .984 1.087 1.012 .472 156 893 .634 .79 150 4370 13440 316 331 225 240 0 8891 607 8284 1.251 8870 8263 .799 1.208 .323 .273
7 10854 10302 1697 486 9157 9816 11504 11799 1906 599 9807 11313 0 0 4985 5028 2743 1270 85 92 72 88 18973 21120 .933 1.072 1.154 1.579 1.075 3.279 156 821 .858 .83 140 4580 13440 317 331 247 261 0 12653 597 12056 1.317 14491 13894 .76 1.417 .397 .503
8 11996 11744 1734 481 10262 11263 13432 13505 1776 526 11698 13024 0 0 3720 4064 450 228 100 100 98 100 21525 24722 .911 1.098 1.113 1.218 1.113 .639 156 830 1.041 .94 140 4800 13430 316 330 269 283 0 14424 591 13833 1.348 16586 15996 .742 1.367 .431 .451
9 7556 6374 1719 462 5837 5912 7654 6322 1745 483 5935 5860 0 0 3023 3110 453 162 97 100 95 97 11749 11795 .987 1.013 .987 1.185 1.025 .803 120 631 .916 .9 120 5020 13430 317 329 292 304 0 7828 567 7261 1.244 7764 7197 .804 1.213 .315 .278
10 10177 9907 1724 466 8453 9441 11803 11005 1782 539 10079 10539 0 0 4382 4561 470 374 97 99 95 98 17894 20618 .895 1.117 1.046 1.374 1.116 1.428 208 1032 1.036 .95 160 5220 13440 316 332 310 326 0 12167 572 11595 1.372 13516 12944 .729 1.284 .456 .361
11 19880 19001 1750 474 18130 18527 21758 21536 1803 568 20008 21062 0 0 5443 7199 465 430 100 100 100 100 36657 41070 .979 1.022 1.053 1.117 1.038 .768 120 685 .984 .92 130 5450 13440 317 330 334 347 0 23336 582 22754 1.255 26450 25868 .797 1.293 .328 .371
12 9170 8191 1752 480 7418 7711 9563 8859 1797 573 7811 8379 0 0 2378 2536 507 321 99 99 98 98 15129 16190 .962 1.039 1.073 1.155 1.03 .686 156 931 .963 .92 150 5660 13430 315 330 354 369 0 10060 590 9470 1.277 10880 10291 .783 1.317 .352 .398
13 13212 12118 1881 508 11331 11610 13636 13084 1924 599 11755 12576 0 0 3084 3564 543 371 99 100 98 100 22941 24331 .976 1.025 1.07 1.13 1.041 .626 120 723 .97 .92 130 5880 13440 317 330 377 390 0 14883 624 14259 1.258 16069 15445 .795 1.314 .332 .394
14 13219 13216 1862 512 11357 12704 14170 14656 1920 575 12308 14144 0 0 3788 3897 561 332 100 100 99 100 24061 26452 .894 1.119 1.149 1.21 1.123 .454 120 634 1.038 .94 120 6090 13440 318 330 399 411 0 16231 629 15603 1.374 18000 17371 .728 1.411 .458 .497
15 13597 12815 1853 470 11744 12345 14231 14048 1893 549 12378 13578 0 0 5062 5229 551 379 100 100 99 100 24089 25956 .951 1.051 1.097 1.148 1.109 .517 120 626 .981 .93 120 6300 13440 318 330 420 432 0 15739 577 15162 1.291 17253 16676 .775 1.347 .369 .43
16 10727 10045 1746 483 8981 9562 10958 10659 1777 516 9212 10176 0 0 4285 4396 408 181 100 100 100 100 18543 19388 .939 1.065 1.105 1.225 1.053 .804 120 693 .95 .91 120 6520 13440 318 330 442 454 0 12337 593 11744 1.308 13091 12498 .765 1.357 .387 .44
17 11107 10093 1742 498 9365 9595 11684 10703 1777 546 9942 10205 0 0 3598 3401 454 233 100 100 98 100 18960 20147 .976 1.025 1.026 1.224 1.02 1.251 80 596 .918 .92 110 6740 13430 317 328 464 475 0 12396 612 11784 1.258 13145 12533 .795 1.261 .332 .334
18 4193 2384 1791 494 2402 1890 4321 2346 1868 602 2530 1852 0 0 1113 894 663 681 90 91 83 72 4292 4382 1.271 .787 .732 1.146 .738 2.495 120 689 .638 .77 120 6960 13430 317 329 486 498 0 2928 607 2321 .966 2881 2275 1.035 .899 -.049 -.154
19 13349 11484 1804 531 11545 10953 13602 11893 1908 736 11798 11362 0 0 2810 3153 816 1142 100 98 100 97 22498 23160 1.054 .949 .963 .976 1.007 .297 80 580 .9 .92 110 7160 13420 316 327 506 517 0 14104 652 13452 1.165 14607 13954 .858 1.183 .221 .242
20 8667 7869 1667 490 7000 7379 8542 9098 1703 496 6875 8608 0 0 3260 3548 415 124 100 100 96 100 14379 15483 .949 1.054 1.252 1.167 1.025 .676 52 340 .931 .87 80 7370 13450 321 329 529 537 0 9664 602 9063 1.295 11174 10572 .772 1.538 .373 .621

Total number of rows: 8320

Table truncated, full table size 2023 Kbytes.




Supplementary data files not provided
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