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Sample GSM87466 Query DataSets for GSM87466
Status Public on Dec 15, 2005
Title delPPT1_hypo_osmotic_shock_60min
Sample type RNA
 
Channel 1
Source name delPPT1(mid-lgo on YPD, 30C, OD 0.39)
Organism Saccharomyces cerevisiae
Characteristics delPPT1(mid-lgo on YPD, 30C, OD 0.39)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name delPPT1, 60min after transfer to regular YPD
Organism Saccharomyces cerevisiae
Characteristics delPPT1, 60min after transfer to regular YPD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34356.gif
Measurement: time(absolute) 60 m
name: 34356_Time
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 Dec 13, 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 GPL2638
Series (1)
GSE3812 Response of yeast cells to stress

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 5790 8936 94 95 5696 8841 6042 9162 101 108 5948 9067 0 0 1623 2683 33 56 100 100 100 100 14537 15015 .644 1.552 1.524 1.572 1.542 1.206 120 708 1.562 .99 120 2130 9740 100 112 47 59 0 11758 125 11633 2.042 12055 11930 .49 2.006 1.03 1.004
2 3541 3558 97 101 3444 3457 3607 3542 108 119 3510 3441 0 0 632 659 40 63 100 100 100 100 6901 6951 .996 1.004 .98 1.006 1.004 1.11 120 640 1.001 .99 120 2330 9740 100 112 67 79 0 4682 133 4549 1.321 4661 4528 .757 1.29 .401 .367
3 324 344 83 81 241 263 333 337 98 100 250 256 0 0 72 85 72 92 97 96 90 84 504 506 .916 1.091 1.024 1.11 1.073 1.449 120 654 1.117 .93 120 2520 9740 100 112 86 98 0 453 107 346 1.436 443 337 .696 1.347 .522 .43
4 4914 3652 75 69 4839 3583 5252 3844 83 74 5177 3775 0 0 1122 767 31 27 100 100 100 100 8422 8952 1.351 .74 .729 .749 .734 1.121 120 696 .737 .99 130 2720 9740 99 112 105 118 0 4805 91 4714 .974 5058 4967 1.026 .959 -.038 -.06
5 296 269 75 69 221 200 308 277 81 73 233 208 0 0 73 75 25 26 99 98 98 96 421 441 1.105 .905 .893 .876 .906 1.485 120 638 .951 .91 120 2920 9740 100 112 126 138 0 354 91 263 1.191 364 274 .84 1.175 .252 .232
6 868 1002 74 68 794 934 892 1026 79 73 818 958 0 0 228 219 28 26 100 100 100 100 1728 1776 .85 1.176 1.171 1.2 1.186 1.229 120 651 1.163 .98 120 3130 9740 100 112 147 159 0 1318 89 1229 1.548 1350 1261 .646 1.541 .63 .624
7 208 172 75 69 133 103 215 170 81 78 140 101 0 0 49 50 34 93 95 59 90 7 236 241 1.291 .774 .721 .741 .816 1.733 120 628 .762 .84 120 3340 9730 99 111 168 180 0 226 91 136 1.019 224 133 .981 .949 .027 -.075
8 4181 2982 81 78 4100 2904 4321 3111 88 83 4240 3033 0 0 824 585 30 31 100 100 100 100 7004 7273 1.412 .708 .715 .71 .708 1.1 120 609 .711 .99 120 3530 9740 100 112 187 199 0 3924 103 3821 .932 4093 3991 1.073 .941 -.102 -.087
9 1157 1623 85 84 1072 1539 1221 1690 94 91 1136 1606 0 0 270 365 40 39 100 100 100 100 2611 2742 .697 1.436 1.414 1.454 1.435 1.16 120 654 1.446 .99 120 3730 9740 100 112 207 219 0 2136 111 2025 1.889 2224 2113 .529 1.86 .918 .895
10 398 357 78 74 320 283 393 360 88 83 315 286 0 0 131 113 68 46 96 98 91 95 603 601 1.131 .884 .908 .9 .878 1.391 120 644 .858 .95 120 3930 9740 100 112 227 239 0 470 97 372 1.164 474 376 .859 1.195 .219 .257
11 605 504 76 72 529 432 609 516 159 115 533 444 0 0 222 191 944 449 3 48 0 0 961 977 1.225 .817 .833 .816 .822 1.357 120 660 .822 .97 120 4140 9720 98 110 248 260 0 663 95 568 1.075 679 584 .931 1.096 .104 .132
12 201 165 77 71 124 94 202 167 84 75 125 96 0 0 50 47 30 25 97 94 89 83 218 221 1.319 .758 .768 .708 .686 1.734 120 674 .734 .82 120 4340 9720 98 110 268 280 0 217 93 124 .997 220 126 1.003 1.011 -.004 .015
13 429 423 76 69 353 354 421 414 82 73 345 345 0 0 112 114 22 24 100 100 100 100 707 690 .997 1.003 1 1.006 1.02 1.345 80 572 .966 .93 110 4540 9720 98 109 288 299 0 557 91 466 1.32 545 454 .758 1.316 .4 .396
14 619 655 76 72 543 583 638 667 83 75 562 595 0 0 133 161 37 26 100 100 100 100 1126 1157 .931 1.074 1.059 1.063 1.078 1.246 120 655 1.091 .96 120 4750 9730 99 111 309 321 0 862 95 767 1.413 878 783 .708 1.393 .498 .478
15 5782 4986 84 78 5698 4908 5887 5089 102 91 5803 5011 0 0 1611 1189 63 48 100 100 100 100 10606 10814 1.161 .861 .864 .87 .872 1.105 120 666 .843 .99 130 4950 9740 99 112 328 341 0 6561 103 6458 1.133 6696 6593 .882 1.136 .181 .184
16 843 1082 102 99 741 983 875 1076 142 145 773 977 0 0 217 283 129 157 99 99 98 98 1724 1750 .754 1.327 1.264 1.349 1.312 1.27 120 652 1.303 .96 120 5150 9730 99 111 349 361 0 1424 130 1293 1.746 1416 1286 .573 1.663 .804 .734
17 652 735 114 120 538 615 643 734 137 153 529 614 0 0 193 218 77 102 98 100 96 97 1153 1143 .875 1.143 1.161 1.155 1.12 1.249 80 561 1.137 .96 110 5340 9720 98 109 368 379 0 967 158 809 1.504 966 808 .665 1.527 .589 .611
18 1607 1987 106 108 1501 1879 1603 1972 122 125 1497 1864 0 0 533 667 65 68 100 100 100 100 3380 3361 .799 1.252 1.245 1.254 1.257 1.125 120 653 1.255 .99 120 5550 9720 98 110 389 401 0 2614 142 2472 1.647 2595 2453 .607 1.638 .72 .712
19 411 367 100 95 311 272 385 332 111 105 285 237 0 0 153 144 50 45 99 99 97 94 583 522 1.143 .875 .832 .858 .884 1.382 120 629 .89 .95 120 5750 9730 99 111 409 421 0 483 125 358 1.151 437 312 .869 1.094 .203 .13
20 481 393 95 88 386 305 482 387 105 95 387 299 0 0 159 137 63 43 99 98 92 93 691 686 1.266 .79 .773 .784 .781 1.36 120 644 .787 .95 120 5940 9730 99 111 428 440 0 517 116 401 1.04 509 393 .962 1.017 .056 .024

Total number of rows: 6912

Table truncated, full table size 1482 Kbytes.




Supplementary data files not provided
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