NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM87465 Query DataSets for GSM87465
Status Public on Dec 15, 2005
Title delPPT1_hypo_osmotic_shock_30min
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, 30min after transfer to regular YPD
Organism Saccharomyces cerevisiae
Characteristics delPPT1, 30min after transfer to regular YPD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34355.gif
Measurement: time(absolute) 30 m
name: 34355_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 4064 5865 69 63 3995 5802 4373 6268 74 67 4304 6205 0 0 1159 1520 35 38 100 100 100 100 9797 10509 .689 1.452 1.442 1.491 1.44 1.293 120 685 1.428 .98 120 2160 9600 86 98 50 62 0 7519 81 7438 1.862 8036 7955 .537 1.848 .897 .886
2 3042 2547 71 64 2971 2483 3111 2602 76 70 3040 2538 0 0 558 500 38 42 100 100 100 100 5454 5578 1.197 .836 .835 .829 .831 1.223 120 649 .831 .99 120 2360 9590 85 97 70 82 0 3265 82 3183 1.071 3336 3254 .933 1.07 .1 .098
3 314 332 70 65 244 267 304 324 76 71 234 259 0 0 63 76 31 35 100 100 100 98 511 493 .914 1.094 1.107 1.079 1.145 1.435 80 557 1.118 .91 110 2550 9590 85 96 89 100 0 426 83 342 1.403 415 332 .713 1.419 .488 .505
4 4396 3693 69 61 4327 3632 4803 3944 72 65 4734 3883 0 0 1205 1005 20 23 100 100 100 100 7959 8617 1.191 .839 .82 .844 .846 1.191 120 683 .838 .99 120 2750 9600 86 98 109 121 0 4735 78 4656 1.076 5056 4978 .929 1.052 .106 .073
5 298 249 70 64 228 185 299 241 74 66 229 177 0 0 63 60 19 20 100 98 100 97 413 406 1.232 .811 .773 .794 .786 1.377 80 604 .855 .93 110 2960 9580 84 95 130 141 0 319 82 237 1.04 309 227 .961 .991 .057 -.013
6 1071 1103 71 64 1000 1039 1107 1138 82 77 1036 1074 0 0 218 237 63 84 100 100 100 100 2039 2110 .962 1.039 1.037 1.033 1.057 1.183 80 598 1.027 .98 110 3160 9580 84 95 150 161 0 1414 82 1332 1.332 1459 1377 .751 1.329 .414 .41
7 236 212 70 64 166 148 242 214 77 71 172 150 0 0 47 46 35 42 97 100 93 91 314 322 1.122 .892 .872 .908 .91 1.572 80 591 .881 .88 110 3360 9570 83 94 170 181 0 272 82 190 1.143 274 192 .875 1.118 .193 .161
8 5329 3716 77 70 5252 3646 5757 4036 87 79 5680 3966 0 0 1323 951 40 37 100 100 100 100 8898 9646 1.44 .694 .698 .691 .695 1.166 120 681 .693 .99 120 3560 9590 85 97 190 202 0 4764 90 4674 .89 5174 5085 1.124 .895 -.168 -.16
9 1353 1882 79 74 1274 1808 1415 1895 92 82 1336 1821 0 0 235 351 43 35 100 100 100 100 3082 3157 .705 1.419 1.363 1.42 1.398 1.166 80 571 1.4 .98 110 3750 9590 85 96 209 220 0 2413 95 2318 1.819 2429 2335 .55 1.747 .863 .805
10 428 392 73 67 355 325 411 379 79 72 338 312 0 0 116 127 26 25 100 100 100 100 680 650 1.092 .915 .923 .895 .923 1.346 80 590 .866 .93 110 3950 9590 85 96 229 240 0 503 86 417 1.174 486 400 .852 1.183 .231 .243
11 708 638 74 69 634 569 692 652 84 76 618 583 0 0 219 186 42 40 100 100 100 100 1203 1201 1.114 .897 .943 .897 .881 1.276 80 586 .856 .96 110 4160 9570 83 94 250 261 0 818 88 729 1.151 836 747 .869 1.209 .202 .274
12 196 168 74 67 122 101 181 164 82 73 107 97 0 0 69 52 30 27 93 93 84 80 223 204 1.208 .828 .907 .83 .861 2.199 120 684 .775 .79 120 4360 9580 84 96 270 282 0 215 86 129 1.061 210 124 .942 1.162 .086 .217
13 727 668 77 70 650 598 702 650 88 79 625 580 0 0 255 222 54 37 100 100 100 100 1248 1205 1.087 .92 .928 .937 .869 1.449 80 500 .901 .94 100 4560 9580 85 95 291 301 0 856 90 767 1.179 833 744 .848 1.19 .238 .251
14 1154 1182 81 74 1073 1108 1118 1155 100 90 1037 1081 0 0 371 364 81 84 100 100 100 100 2181 2118 .968 1.033 1.042 1.044 1.065 1.301 80 581 1.025 .96 110 4750 9570 83 94 309 320 0 1515 95 1421 1.324 1481 1386 .755 1.336 .405 .418
15 6393 7539 85 79 6308 7460 6237 7256 102 94 6152 7177 0 0 2590 2779 61 64 100 100 99 100 13768 13329 .846 1.183 1.167 1.231 1.161 1.338 120 612 1.147 .98 120 4960 9600 86 98 330 342 0 9665 101 9564 1.516 9303 9201 .66 1.496 .6 .581
16 1069 1332 84 79 985 1253 1108 1338 103 96 1024 1259 0 0 323 372 61 57 100 100 100 100 2238 2283 .786 1.272 1.229 1.298 1.29 1.304 120 639 1.238 .96 120 5160 9590 85 97 350 362 0 1708 101 1606 1.631 1715 1614 .613 1.576 .706 .657
17 698 693 84 82 614 611 653 670 106 100 569 588 0 0 291 255 77 71 100 100 98 100 1225 1157 1.005 .995 1.033 1.034 .998 1.416 80 550 .981 .94 110 5350 9590 85 96 369 380 0 888 105 783 1.276 859 754 .784 1.325 .351 .406
18 1040 1124 87 86 953 1038 993 1041 112 100 906 955 0 0 389 440 73 54 100 100 100 100 1991 1861 .918 1.089 1.054 1.083 1.044 1.217 120 670 1.085 .96 120 5560 9590 85 97 390 402 0 1441 110 1331 1.396 1335 1224 .716 1.351 .482 .434
19 222 200 83 82 139 118 207 193 107 94 124 111 0 0 72 77 79 54 90 77 28 50 257 235 1.178 .849 .895 .754 .799 1.975 80 566 .728 .81 110 5760 9580 84 95 410 421 0 256 105 151 1.088 247 142 .919 1.148 .122 .199
20 392 311 80 76 312 235 395 309 97 84 315 233 0 0 113 79 53 39 98 100 98 97 547 548 1.328 .753 .74 .765 .758 1.432 80 571 .657 .86 110 5960 9580 84 95 430 441 0 399 97 301 .966 396 299 1.036 .948 -.05 -.077

Total number of rows: 6912

Table truncated, full table size 1475 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap