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Sample GSM90167 Query DataSets for GSM90167
Status Public on Dec 30, 2005
Title Hydrostatic pressure (C1 vs P1)
Sample type RNA
 
Channel 1
Source name C1
Organism Saccharomyces cerevisiae
Characteristics C1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name pressurized cells P1
Organism Saccharomyces cerevisiae
Characteristics P1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Starvation, YPD-stationary-phase
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14947.gif
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 29, 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 GPL2658
Series (1)
GSE3935 Response to high hydrostatic pressure

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 3757 2302 2356 1583 1401 719 3667 2201 2362 1594 1311 618 0 0 772 571 342 324 93 75 81 48 2120 1929 1.949 .513 .471 .505 .53 2.238 316 2327 .952 .65 105 2830 18510 99 120 123 144 0 3713 2553 1160 .828 3550 997 1.208 .76 -.273 -.395
2 2785 2206 2336 1556 449 650 2786 2078 2348 1598 450 522 0 0 468 600 353 365 60 63 25 37 1099 972 .691 1.448 1.16 1.306 1.26 2.738 80 522 2.348 .48 50 3000 18500 103 113 163 173 0 3558 2510 1048 2.335 3352 842 .428 1.871 1.223 .904
3 3741 2354 2301 1560 1440 794 3664 2185 2324 1575 1363 625 0 0 687 789 318 320 96 72 89 48 2234 1988 1.814 .551 .459 .473 .542 2.46 120 940 1.318 .62 65 3175 18510 103 116 196 209 0 3797 2516 1281 .889 3524 1008 1.124 .74 -.169 -.435
4 2589 1946 2318 1554 271 392 2478 1812 2337 1581 160 258 0 0 556 580 338 365 36 41 15 20 663 418 .691 1.446 1.613 1.173 1.176 3.835 316 2215 2.759 .38 100 3350 18510 100 120 228 248 -50 3139 2506 632 2.333 2923 416 .429 2.601 1.222 1.379
5 2489 1753 2273 1544 216 209 2353 1637 2285 1564 80 93 0 0 613 586 318 306 31 28 18 15 425 173 1.033 .968 1.163 .841 .84 3.448 316 2154 2.502 .38 100 3525 18510 100 120 263 283 -50 2827 2490 337 1.561 2640 150 .641 1.875 .642 .907
6 2527 1872 2240 1491 287 381 2409 1759 2231 1500 169 268 0 0 562 609 324 316 36 45 18 23 668 437 .753 1.328 1.586 1.095 1.065 3.4 316 2129 2.491 .43 100 3700 18510 100 120 298 318 -50 3019 2405 615 2.141 2837 432 .467 2.558 1.098 1.355
7 2527 1731 2135 1369 392 362 2438 1618 2122 1369 303 249 0 0 496 520 375 364 43 38 20 18 754 552 1.083 .923 .822 .924 .949 4.011 316 2128 2.659 .38 100 3875 18510 100 120 333 353 -50 2792 2208 584 1.489 2610 402 .671 1.325 .575 .406
8 2196 1450 2196 1414 0 36 2209 1428 2205 1433 13 14 0 0 328 302 326 295 16 20 2 4 36 27 null null 1.077 .853 .82 3.712 316 2121 10.714 .08 100 4050 18510 100 120 368 388 -50 2339 2281 58 null 2303 23 null 1.737 null .797
9 2174 1526 2284 1477 -110 49 2145 1475 2295 1481 -139 -2 0 0 333 393 320 296 10 18 1 5 -61 -141 null null null .745 .702 4.018 316 2046 19.01 .05 100 4220 18510 100 120 402 422 -50 2461 2382 79 null 2379 null null null null null
10 2322 1486 2276 1486 46 0 2330 1469 2284 1510 54 -17 0 0 312 284 323 357 20 10 2 1 46 37 null null null .751 .848 3.518 316 2141 7.025 .15 100 4395 18510 100 120 437 457 -50 2397 2397 0 null 2369 null null null null null
11 2341 1598 2284 1550 57 48 2309 1552 2299 1572 25 2 0 0 353 358 330 313 20 19 3 6 105 27 1.188 .842 .08 .791 .973 4.403 316 2128 17.392 .05 100 4570 18510 100 120 472 492 -50 2577 2500 77 1.358 2503 3 .736 .129 .442 -2.954
12 2329 1551 2268 1528 61 23 2331 1530 2277 1549 63 2 0 0 315 311 331 322 18 16 3 3 84 65 2.652 .377 .032 1.202 1.041 4.79 316 2106 15.054 .06 100 4745 18510 100 120 507 527 -50 2502 2465 37 .608 2468 3 1.644 .051 -.718 -4.288
13 2338 1613 2227 1519 111 94 2302 1617 2240 1540 75 98 0 0 334 308 331 329 23 22 6 3 205 173 1.181 .847 1.307 .949 1.021 4.092 316 2092 -1 -1 100 4915 18510 100 120 541 561 -50 2602 2450 152 1.366 2608 158 .732 2.108 .45 1.076
14 2114 1475 2161 1476 -47 -1 2091 1415 2184 1501 -70 -61 0 0 376 383 335 352 12 10 2 2 -48 -131 null null null 1.029 .985 4.233 316 2141 12.185 .08 100 5090 18510 100 120 576 596 -50 2379 2381 -2 null 2282 null null null null null
15 2256 1608 2084 1507 172 101 2230 1567 2097 1516 146 60 0 0 370 412 358 373 30 21 7 5 273 206 1.703 .587 .411 1.025 1.057 4.316 316 2152 8.173 .12 100 5265 18510 100 120 611 631 -50 2594 2431 163 .947 2527 97 1.056 .663 -.078 -.593
16 2063 1579 2075 1573 -12 6 2074 1568 2088 1586 -1 -5 0 0 296 321 310 307 14 17 1 4 -6 -6 null null null 1.188 1.274 3.728 316 2121 -1 -1 100 5440 18510 100 120 646 666 -50 2547 2537 10 null 2529 null null null null null
17 4502 4178 2130 1630 2372 2548 2197 1831 2538 1960 67 201 1 1 10279 10527 4086 3829 6 6 5 6 4920 268 .931 1.074 3 1.144 1.11 3.736 316 2122 1.019 .96 100 5610 18510 100 120 680 700 -50 6739 2629 4110 1.733 2953 324 .577 4.839 .793 2.275
18 1780 1261 2119 1572 -339 -311 1808 1299 2155 1580 -311 -273 0 0 392 410 795 334 0 5 0 0 -650 -584 null null null 1.061 1.076 2.938 316 2127 2.675 .39 100 5785 18515 101 121 715 735 -50 2034 2535 -502 null 2095 null null null null null
19 2150 1468 2165 1550 -15 -82 2133 1473 2180 1557 -32 -77 0 0 376 355 347 343 16 10 2 1 -97 -109 null null null .877 1.007 3.709 316 2079 3.435 .28 100 5960 18515 101 121 750 770 -50 2368 2500 -132 null 2376 null null null null null
20 2349 1567 2281 1555 68 12 2330 1540 2287 1570 49 -15 0 0 317 333 353 326 17 16 2 3 80 34 5.667 .176 null 1.158 1.101 4.057 316 2120 42.098 .03 100 6135 18515 101 121 785 805 -50 2527 2508 19 .285 2484 null 3.513 null -1.813 null

Total number of rows: 8064

Table truncated, full table size 1926 Kbytes.




Supplementary data files not provided

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