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Sample GSM90166 Query DataSets for GSM90166
Status Public on Dec 30, 2005
Title Hydrostatic pressure (C2 vs P2)
Sample type RNA
 
Channel 1
Source name C2
Organism Saccharomyces cerevisiae
Characteristics C2
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name pressurized cells P2
Organism Saccharomyces cerevisiae
Characteristics P2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Starvation, YPD-stationary-phase
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14946.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 4037 2461 2125 1220 1912 1241 3929 2359 2236 1416 1804 1139 0 0 1083 741 1108 1831 76 21 34 0 3153 2943 1.541 .649 .631 .637 .672 2.044 460 2410 1.013 .73 120 2815 18880 60 84 71 95 0 3516 1743 1773 .927 3370 1627 1.078 .902 -.109 -.149
2 2629 1440 2271 1323 358 117 2427 1303 2340 1532 156 -20 0 0 1681 1062 702 1603 20 1 5 0 475 136 3.06 .327 null .682 .69 4.295 316 2091 1.358 .64 100 3000 18875 61 81 110 130 -50 2057 1890 167 .467 1861 null 2.142 null -1.099 null
3 3899 2558 2256 1258 1643 1300 3774 2386 2312 1438 1518 1128 0 0 1178 1280 589 1226 87 44 63 7 2943 2646 1.264 .791 .743 .743 .784 2.21 392 2200 1.968 .68 110 3175 18885 62 84 144 166 0 3654 1797 1857 1.13 3409 1611 .885 1.062 .177 .086
4 3419 1599 2305 1242 1114 357 3429 1500 2338 1322 1124 258 0 0 805 510 450 533 80 23 61 8 1471 1382 3.12 .32 .23 .377 .372 2.673 80 538 1.551 .4 50 3360 18875 66 76 187 197 0 2284 1774 510 .458 2143 369 2.184 .328 -1.127 -1.609
5 3928 1810 2370 1299 1558 511 3966 1769 2424 1358 1596 470 0 0 730 529 484 538 92 45 81 16 2069 2066 3.049 .328 .294 .356 .362 2.509 80 656 1.793 .38 55 3535 18880 66 77 221 232 0 2586 1856 730 .469 2527 671 2.134 .421 -1.094 -1.249
6 3307 1529 2301 1214 1006 315 3221 1502 2313 1220 920 288 0 0 703 427 391 353 80 41 60 12 1321 1208 3.194 .313 .313 .379 .425 2.831 80 560 1.551 .39 50 3710 18890 69 79 257 267 0 2184 1734 450 .447 2146 411 2.236 .447 -1.161 -1.161
7 4934 2894 2352 1213 2582 1681 4985 2911 2389 1271 2633 1698 0 0 1055 875 588 496 95 90 88 81 4263 4331 1.536 .651 .645 .638 .669 1.862 316 2095 .978 .79 100 3870 18880 62 82 284 304 0 4134 1733 2401 .93 4159 2426 1.075 .921 -.105 -.118
8 2416 1189 2349 1200 67 -11 2429 1154 2472 1375 80 -46 0 0 399 366 1868 2345 0 0 0 0 56 34 null null null .795 .778 3.766 316 2044 12.544 .07 100 4045 18880 62 82 319 339 -50 1699 1714 -16 null 1649 null null null null null
9 2421 1657 2402 1199 19 458 2321 1243 2436 1233 -81 44 0 0 1225 3384 428 582 11 9 1 3 477 -37 .041 24.105 null .831 .796 3.927 316 1986 5.342 .46 100 4220 18880 62 82 354 374 -50 2367 1713 654 34.436 1776 63 .029 null 5.106 null
10 8769 10448 2373 1190 6396 9258 2858 1690 2419 1235 485 500 1 6 13826 18778 539 575 47 48 33 40 15654 985 .691 1.447 1.031 1.499 1.635 4.708 80 575 1.562 .87 55 4330 18875 65 76 380 391 0 14926 1700 13226 2.068 2414 714 .484 1.473 1.048 .559
11 2623 1229 2599 1219 24 10 2614 1203 2622 1243 15 -16 0 0 413 346 435 346 16 16 2 2 34 -1 2.4 .417 null .734 .765 3.964 316 2169 33.505 .03 100 4565 18880 62 82 423 443 -50 1756 1741 14 .595 1719 null 1.68 null -.748 null
12 2764 1303 2755 1292 9 11 2747 1281 2779 1319 -8 -11 0 0 429 349 459 359 14 13 3 3 20 -19 .818 1.222 null .824 .841 4.461 316 2087 -1 -1 100 4740 18880 62 82 458 478 -50 1861 1846 16 1.746 1830 null .573 null .804 null
13 2826 1400 2840 1473 -14 -73 2801 1377 2880 1512 -39 -96 0 0 424 379 499 439 11 8 0 0 -87 -135 null null null .937 1.021 3.734 316 2046 -29.96 -.03 100 4915 18880 62 82 493 513 -50 2000 2104 -104 null 1967 null null null null null
14 3561 2068 3398 1960 163 108 3537 2039 3402 1978 139 79 0 0 582 532 585 513 19 17 5 4 271 218 1.509 .663 .568 .875 .995 4.245 316 2066 10.894 .09 100 5090 18880 62 82 528 548 -50 2954 2800 154 .947 2913 113 1.056 .812 -.079 -.301
15 3831 2240 3880 2220 -49 20 3843 2215 3920 2245 -37 -5 0 0 516 499 546 505 12 16 1 3 -29 -42 null null null .843 .893 4.95 316 2047 -1 -1 100 5265 18880 62 82 563 583 -50 3200 3171 29 null 3164 null null null null null
16 4073 2359 4034 2281 39 78 4038 2323 3980 2287 4 42 0 0 506 495 705 595 8 12 0 2 117 46 .5 2 10.5 1.085 1.111 4.213 316 2069 -1 -1 100 5435 18880 62 82 597 617 -50 3370 3259 111 2.857 3319 60 .35 15 1.515 3.907
17 4188 2365 3995 2247 193 118 4140 2366 3711 2148 145 119 0 0 558 468 1172 765 4 9 0 0 311 264 1.636 .611 .821 .734 .852 4.79 316 2066 -31.394 -.03 100 5610 18880 62 82 632 652 -50 3379 3210 169 .873 3380 170 1.145 1.172 -.195 .229
18 4001 2509 4018 2259 -17 250 3985 2496 3648 2130 -33 237 0 0 557 517 1350 888 1 11 0 0 233 204 null null null .894 .823 3.998 316 2110 1.058 .64 100 5785 18880 62 82 667 687 -50 3584 3227 357 null 3566 339 null null null null
19 3878 2397 4147 2323 -269 74 4077 2536 3753 2225 -70 213 0 0 1072 759 1383 998 0 7 0 0 -195 143 null null null .832 .709 3.657 316 2062 .98 .77 100 5960 18880 62 82 702 722 -50 3424 3319 106 null 3623 304 null null null null
20 2850 1874 4128 2441 -1278 -567 3585 1849 3912 2367 -543 -592 0 0 1895 2342 1217 910 2 5 1 2 -1845 -1135 null null null .734 .607 2.571 316 2140 1.808 .75 100 6135 18880 62 82 737 757 -50 2677 3487 -810 null 2641 null null null null null

Total number of rows: 8064

Table truncated, full table size 1931 Kbytes.




Supplementary data files not provided

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