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Sample GSM87463 Query DataSets for GSM87463
Status Public on Dec 15, 2005
Title delPPT1_hypo_osmotic_shock_7min
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, 7min after transfer to regular YPD
Organism Saccharomyces cerevisiae
Characteristics delPPT1, 7min after transfer to regular YPD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34353.gif
Measurement: time(absolute) 7 m
name: 34353_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 5891 8939 93 83 5798 8856 6094 9392 112 114 6001 9309 0 0 1847 2741 73 231 100 100 100 100 14654 15310 .655 1.527 1.551 1.544 1.556 1.145 120 712 1.525 .97 120 2110 9720 122 134 53 65 0 11460 106 11354 1.958 12041 11935 .511 1.989 .97 .992
2 3488 3249 105 112 3383 3137 3329 3005 144 169 3224 2893 0 0 993 998 128 265 100 100 100 100 6520 6117 1.078 .927 .897 .922 .912 1.177 120 628 .908 .97 120 2320 9720 122 134 74 86 0 4165 144 4022 1.189 3853 3709 .841 1.15 .25 .202
3 490 505 102 111 388 394 462 466 143 159 360 355 0 0 215 258 126 138 93 88 73 65 782 715 .985 1.015 .986 .912 .97 1.681 120 757 1.038 .83 130 2510 9710 120 133 92 105 0 647 142 505 1.302 597 455 .768 1.264 .381 .338
4 4803 4797 95 95 4708 4702 4791 4924 130 128 4696 4829 0 0 1751 1793 107 96 100 100 100 100 9410 9525 1.001 .999 1.028 1.004 1.003 1.2 120 645 .996 .98 120 2720 9730 123 135 114 126 0 6150 122 6028 1.28 6313 6191 .781 1.318 .357 .399
5 470 451 94 94 376 357 456 395 121 125 362 301 0 0 167 211 74 92 98 100 97 86 733 663 1.053 .949 .831 .914 .925 1.445 80 564 1.097 .87 110 2920 9710 121 132 134 145 0 578 121 458 1.217 506 386 .822 1.066 .284 .092
6 680 742 92 92 588 650 687 739 118 120 595 647 0 0 180 178 73 88 99 99 97 96 1238 1242 .905 1.105 1.087 1.131 1.074 1.369 120 725 1.1 .93 130 3120 9720 121 134 153 166 0 951 118 833 1.417 947 829 .706 1.394 .503 .479
7 213 182 88 84 125 98 206 179 109 102 118 95 0 0 58 64 67 65 82 61 38 30 223 213 1.276 .784 .805 .693 .779 2.11 120 710 .933 .64 130 3320 9710 120 133 173 186 0 233 108 126 1.005 229 122 .995 1.032 .007 .046
8 3096 2252 86 82 3010 2170 3197 2341 107 96 3111 2259 0 0 720 528 66 56 100 100 100 100 5180 5370 1.387 .721 .726 .72 .72 1.131 120 661 .728 .97 120 3510 9720 122 134 193 205 0 2887 105 2782 .924 3001 2896 1.082 .931 -.114 -.103
9 898 1149 87 83 811 1066 924 1147 117 117 837 1064 0 0 167 200 96 142 100 100 100 100 1877 1901 .761 1.314 1.271 1.321 1.28 1.235 80 581 1.317 .95 110 3710 9700 120 131 213 224 0 1473 106 1367 1.685 1471 1364 .593 1.63 .753 .705
10 359 300 84 83 275 217 357 275 104 99 273 192 0 0 100 112 66 77 97 95 92 71 492 465 1.267 .789 .703 .746 .728 1.552 80 589 .838 .86 110 3900 9710 121 132 232 243 0 385 106 278 1.012 353 246 .988 .902 .017 -.149
11 454 361 83 77 371 284 453 355 99 88 370 278 0 0 153 121 47 41 98 97 96 93 655 648 1.306 .765 .751 .753 .772 1.513 80 593 .762 .91 110 4110 9700 120 131 253 264 0 463 99 364 .981 455 356 1.019 .963 -.027 -.054
12 173 141 81 73 92 68 164 138 93 84 83 65 0 0 52 45 41 42 85 68 50 35 160 148 1.353 .739 .783 .694 .768 2.084 120 676 .78 .62 120 4310 9710 121 133 273 285 0 181 94 87 .948 177 83 1.055 1.004 -.078 .006
13 356 323 82 74 274 249 357 325 90 80 275 251 0 0 105 86 36 32 98 100 96 100 523 526 1.1 .909 .913 .936 .914 1.54 80 560 .925 .89 110 4510 9710 121 132 293 304 0 414 95 319 1.165 417 322 .858 1.17 .22 .227
14 524 582 81 73 443 509 543 604 90 79 462 531 0 0 124 151 32 28 100 99 99 98 952 993 .87 1.149 1.149 1.146 1.147 1.245 120 670 1.166 .95 120 4710 9710 121 133 313 325 0 746 94 653 1.473 774 681 .679 1.474 .559 .559
15 3346 3958 82 76 3264 3882 3430 3978 97 83 3348 3902 0 0 817 953 46 32 100 100 100 100 7146 7250 .841 1.189 1.165 1.193 1.179 1.169 120 628 1.21 .96 120 4920 9710 121 133 334 346 0 5074 97 4977 1.525 5100 5003 .656 1.494 .609 .579
16 751 770 83 76 668 694 759 791 96 83 676 715 0 0 215 208 42 35 100 100 99 100 1362 1391 .963 1.039 1.058 1.046 1.036 1.28 120 616 1.047 .95 120 5110 9710 121 133 353 365 0 987 97 890 1.332 1014 917 .751 1.356 .414 .439
17 300 259 84 78 216 181 316 264 96 85 232 186 0 0 86 85 41 36 95 94 90 89 397 418 1.193 .838 .802 .838 .871 1.808 120 629 .887 .88 120 5320 9710 121 133 374 386 0 332 100 232 1.074 338 238 .931 1.028 .103 .04
18 674 626 86 79 588 547 689 637 99 84 603 558 0 0 177 155 45 31 100 100 98 100 1135 1161 1.075 .93 .925 .942 .918 1.359 120 614 .916 .95 120 5520 9710 121 133 394 406 0 803 101 701 1.193 817 715 .838 1.186 .254 .247
19 153 122 87 74 66 48 157 116 100 80 70 42 0 0 84 62 41 30 62 56 44 36 114 112 1.375 .727 .6 .519 .569 2.31 120 722 .654 .71 130 5730 9710 120 133 414 427 0 156 95 62 .932 149 54 1.073 .769 -.101 -.379
20 363 275 82 72 281 203 358 270 92 77 276 198 0 0 112 85 34 29 100 98 100 98 484 474 1.384 .722 .717 .709 .745 1.492 80 543 .72 .89 110 5920 9700 120 131 434 445 0 353 92 260 .926 346 254 1.08 .92 -.111 -.121

Total number of rows: 6912

Table truncated, full table size 1505 Kbytes.




Supplementary data files not provided
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