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Sample GSM87462 Query DataSets for GSM87462
Status Public on Dec 15, 2005
Title delPPT1_hypo_osmotic_shock_0min
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, 0min after transfer to regular YPD
Organism Saccharomyces cerevisiae
Characteristics delPPT1, 0min after transfer to regular YPD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34352.gif
Measurement: time(absolute) 0 m
name: 34352_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 1891 2659 62 63 1829 2596 1826 2608 72 69 1764 2545 0 0 496 731 31 30 100 100 100 100 4425 4309 .705 1.419 1.443 1.421 1.386 1.271 120 799 1.48 .94 130 2180 9260 75 88 59 72 0 3453 82 3371 1.843 3387 3305 .543 1.874 .882 .906
2 1909 1583 62 61 1847 1522 1897 1528 73 70 1835 1467 0 0 503 447 37 44 100 100 100 100 3369 3302 1.214 .824 .799 .827 .815 1.273 120 628 .855 .91 120 2380 9250 75 87 80 92 0 2056 79 1977 1.07 1984 1905 .934 1.038 .098 .054
3 206 173 62 61 144 112 205 171 74 68 143 110 0 0 60 59 42 36 92 90 84 75 256 253 1.286 .778 .769 .731 .78 2.097 120 644 .856 .72 120 2580 9260 76 88 100 112 0 225 79 145 1.01 222 143 .99 .999 .014 -.001
4 2733 2498 64 60 2669 2438 2919 2520 79 69 2855 2460 0 0 931 738 62 45 98 100 98 100 5107 5315 1.095 .913 .862 .995 .885 1.826 120 615 .89 .93 120 2780 9260 76 88 120 132 0 3244 78 3166 1.186 3273 3195 .843 1.119 .246 .162
5 218 194 65 62 153 132 222 191 83 73 157 129 0 0 78 62 55 44 87 94 74 76 285 286 1.159 .863 .822 .896 .816 2.033 120 680 .813 .75 130 2970 9260 75 88 138 151 0 252 81 171 1.12 248 168 .893 1.067 .164 .094
6 688 706 66 61 622 645 727 696 81 70 661 635 0 0 221 210 46 35 98 100 96 99 1267 1296 .964 1.037 .961 1.069 1.019 1.477 120 641 1.089 .89 120 3180 9250 75 87 160 172 0 917 79 838 1.347 904 825 .743 1.248 .429 .319
7 179 138 66 62 113 76 171 132 78 70 105 70 0 0 48 41 38 37 97 80 83 44 189 175 1.487 .673 .667 .613 .721 1.941 120 642 .665 .66 120 3380 9250 75 87 180 192 0 179 81 99 .873 171 91 1.145 .866 -.195 -.208
8 2427 1829 66 65 2361 1764 2601 1859 77 70 2535 1794 0 0 990 550 39 34 97 100 96 100 4125 4329 1.338 .747 .708 .883 .693 2.496 120 612 .693 .91 120 3580 9270 77 89 200 212 0 2375 84 2291 .97 2414 2330 1.031 .919 -.043 -.122
9 736 871 65 63 671 808 732 906 80 70 667 843 0 0 237 261 43 32 99 100 98 100 1479 1510 .83 1.204 1.264 1.241 1.202 1.46 120 658 1.253 .9 120 3780 9250 75 87 220 232 0 1131 82 1049 1.564 1177 1095 .639 1.641 .645 .715
10 238 185 64 61 174 124 241 188 74 65 177 127 0 0 81 62 35 25 96 94 91 87 298 304 1.403 .713 .718 .707 .718 1.9 120 666 .669 .77 120 3980 9260 76 88 240 252 0 240 79 161 .926 244 165 1.08 .932 -.112 -.102
11 379 273 64 63 315 210 370 262 75 68 306 199 0 0 161 90 41 36 100 98 96 97 525 505 1.5 .667 .65 .676 .648 1.538 80 601 .611 .84 110 4180 9230 73 84 260 271 0 355 82 273 .866 340 258 1.155 .845 -.208 -.244
12 161 131 66 62 95 69 149 127 79 67 83 65 0 0 54 37 43 31 88 88 45 51 164 148 1.377 .726 .783 .732 .783 2.015 80 615 .609 .63 110 4390 9240 74 85 281 292 0 170 81 90 .943 165 84 1.06 1.017 -.084 .024
13 321 262 66 63 255 199 323 258 78 67 257 195 0 0 101 84 36 28 97 97 93 96 454 452 1.281 .78 .759 .797 .777 1.97 80 574 .759 .83 110 4590 9240 74 85 301 312 0 340 82 258 1.013 335 253 .987 .985 .019 -.021
14 566 706 68 65 498 641 615 724 79 68 547 659 0 0 172 195 36 25 98 100 97 100 1139 1206 .777 1.287 1.205 1.354 1.274 1.502 120 670 1.304 .94 120 4790 9250 75 87 321 333 0 917 84 832 1.672 940 856 .598 1.565 .741 .646
15 3346 4702 72 70 3274 4632 3704 4734 86 77 3632 4664 0 0 1292 1313 50 41 98 100 97 100 7906 8296 .707 1.415 1.284 1.628 1.347 2.193 120 620 1.385 .91 120 5000 9250 75 87 342 354 0 6106 91 6016 1.837 6148 6057 .544 1.668 .878 .738
16 944 1011 74 73 870 938 978 1054 94 82 904 981 0 0 340 294 67 47 98 100 95 100 1808 1885 .928 1.078 1.085 1.175 1.028 1.962 120 742 1.051 .92 130 5200 9250 74 87 361 374 0 1313 95 1218 1.4 1369 1274 .714 1.409 .486 .495
17 341 275 71 68 270 207 333 269 90 76 262 201 0 0 148 105 59 38 94 96 85 90 477 463 1.304 .767 .767 .816 .734 1.97 120 631 .716 .86 120 5400 9250 75 87 382 394 0 357 88 269 .996 349 261 1.004 .996 -.006 -.005
18 1522 1667 74 71 1448 1596 1622 1720 91 80 1548 1649 0 0 493 486 60 39 100 100 99 100 3044 3197 .907 1.102 1.065 1.132 1.051 1.36 120 640 1.093 .95 120 5600 9240 74 86 402 414 0 2165 92 2073 1.431 2234 2142 .699 1.383 .517 .468
19 334 257 73 70 261 187 330 249 92 78 257 179 0 0 79 76 62 38 100 100 97 97 448 436 1.396 .716 .696 .689 .725 1.473 80 566 .759 .84 110 5800 9240 74 85 422 433 0 334 91 243 .93 323 232 1.075 .905 -.104 -.145
20 364 234 71 65 293 169 359 231 84 71 288 166 0 0 113 74 52 43 100 96 95 88 462 454 1.734 .577 .576 .562 .588 1.602 80 548 .574 .84 110 5980 9240 74 85 440 451 0 304 84 219 .749 300 216 1.335 .749 -.417 -.418

Total number of rows: 6912

Table truncated, full table size 1478 Kbytes.




Supplementary data files not provided
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