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Sample GSM90004 Query DataSets for GSM90004
Status Public on Dec 30, 2005
Title Fraction 64-66 B
Sample type RNA
 
Channel 1
Source name Reference RNA
Organism Saccharomyces cerevisiae
Characteristics Reference RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Fraction 64-66
Organism Saccharomyces cerevisiae
Characteristics Fraction 64-66
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41757.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 GPL3292
Series (1)
GSE3932 Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

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
1 556 153 70 53 486 100 379 135 74 53 309 82 0 0 399 71 19 8 98 96 94 92 586 391 4.86 .206 .265 .221 .205 1.55 52 313 .187 .96 80 1880 17980 18 26 36 44 0 785 272 513 1.056 693 421 .947 1.362 .078 .445
2 14890 122 81 54 14809 68 12899 118 83 54 12818 64 0 0 9263 40 17 8 100 98 100 84 14877 12882 217.779 .005 .005 .014 .012 1.613 52 327 .004 .94 80 2040 17970 17 25 52 60 0 626 277 349 .024 605 328 42.446 .026 -5.408 -5.287
3 19947 8452 71 53 19876 8399 18867 6889 74 54 18796 6836 0 0 9581 4633 16 8 100 100 100 100 28275 25632 2.366 .423 .364 .437 .408 1.706 52 397 .422 .96 90 2220 17970 16 25 69 78 0 43365 272 43094 2.168 35346 35074 .461 1.866 1.116 .9
4 6254 318 66 52 6188 266 7616 352 69 53 7550 300 0 0 2914 107 26 9 100 100 100 93 6454 7850 23.263 .043 .04 .047 .042 1.676 32 236 .04 .95 70 2390 17970 17 24 87 94 0 1632 267 1365 .221 1806 1539 4.534 .204 -2.181 -2.294
5 2466 5317 71 53 2395 5264 2660 5675 76 54 2589 5622 0 0 1216 2617 28 10 100 100 100 100 7659 8211 .455 2.198 2.171 2.264 2.165 1.473 52 410 2.212 .97 90 2570 17970 16 25 104 113 0 27280 272 27009 11.277 29117 28845 .089 11.141 3.495 3.478
6 15974 459 84 56 15890 403 17060 486 89 57 16976 430 0 0 4639 94 21 11 100 100 100 100 16293 17406 39.429 .025 .025 .026 .025 1.221 52 387 .023 .96 90 2750 17970 16 25 122 131 0 2355 287 2068 .13 2494 2206 7.685 .13 -2.942 -2.944
7 2712 996 89 57 2623 939 3050 1095 92 57 2961 1038 0 0 906 257 20 9 100 100 100 100 3562 3999 2.793 .358 .351 .372 .35 1.351 52 322 .338 .97 80 2920 17970 17 25 140 148 0 5110 292 4818 1.837 5618 5326 .544 1.799 .877 .847
8 2116 613 91 56 2025 557 1240 546 96 57 1149 490 0 0 1796 367 25 9 100 100 100 100 2582 1639 3.636 .275 .426 .337 .302 1.632 52 387 .227 .94 90 3090 17970 16 25 156 165 0 3145 287 2858 1.411 2801 2514 .709 2.188 .497 1.13
9 771 391 91 57 680 334 860 431 96 58 769 374 0 0 276 112 29 9 96 100 94 100 1014 1143 2.036 .491 .486 .556 .498 1.628 52 340 .474 .97 80 3270 17970 17 25 175 183 0 2006 292 1714 2.52 2211 1919 .397 2.495 1.333 1.319
10 1079 357 83 57 996 300 884 302 89 57 801 245 0 0 642 172 27 8 100 100 100 100 1296 1046 3.32 .301 .306 .313 .298 1.345 32 236 .284 .97 70 3440 17970 17 24 192 199 0 1832 292 1539 1.545 1549 1257 .647 1.569 .628 .65
11 3228 152 74 55 3154 97 3507 161 79 55 3433 106 0 0 1251 45 22 9 100 98 100 94 3251 3539 32.515 .031 .031 .031 .032 1.422 52 385 .028 .92 90 3620 17980 17 26 209 218 0 780 282 498 .158 826 544 6.337 .158 -2.664 -2.658
12 3971 421 69 54 3902 367 4136 463 73 54 4067 409 0 0 1127 109 18 9 100 100 100 100 4269 4476 10.632 .094 .101 .092 .095 1.355 52 321 .089 .95 80 3790 17970 17 25 227 235 0 2160 277 1883 .483 2376 2098 2.072 .516 -1.051 -.955
13 3501 304 83 58 3418 246 3608 309 86 60 3525 251 0 0 909 56 21 12 100 100 100 100 3664 3776 13.894 .072 .071 .074 .072 1.276 52 378 .067 .96 90 3970 17970 16 25 244 253 0 1560 298 1262 .369 1585 1288 2.708 .365 -1.437 -1.453
14 8705 35745 86 63 8619 35682 9509 36900 89 65 9423 36837 0 0 3584 13274 22 14 100 100 100 100 44301 46260 .242 4.14 3.909 4.605 4.151 1.71 52 384 4.041 .94 90 4130 17960 15 24 260 269 0 183400 323 183077 21.241 189326 189003 .047 20.058 4.409 4.326
15 3365 2322 80 58 3285 2264 3619 2433 83 59 3539 2375 0 0 971 545 28 9 100 100 100 100 5549 5914 1.451 .689 .671 .708 .677 1.256 52 387 .665 .98 90 4310 17970 16 25 278 287 0 11914 298 11616 3.536 12483 12186 .283 3.443 1.822 1.784
16 2454 213 77 57 2377 156 2757 225 81 58 2680 168 0 0 873 50 27 9 100 100 100 100 2533 2848 15.237 .066 .063 .068 .062 1.578 52 379 .059 .94 90 4480 17970 16 25 295 304 0 1093 292 800 .337 1154 862 2.97 .322 -1.57 -1.637
17 1185 164 76 57 1109 107 1231 166 80 58 1155 109 0 0 373 31 21 9 100 100 100 100 1216 1264 10.364 .096 .094 .1 .098 1.418 52 329 .088 .94 80 4650 17970 17 25 313 321 0 841 292 549 .495 852 559 2.02 .484 -1.014 -1.046
18 3558 1033 80 58 3478 975 2301 806 82 60 2221 748 0 0 2879 657 19 11 100 100 100 100 4453 2969 3.567 .28 .337 .343 .301 1.733 52 328 .248 .96 80 4830 17970 17 25 331 339 0 5300 298 5003 1.438 4135 3838 .695 1.728 .524 .789
19 5611 1460 78 58 5533 1402 6442 1592 80 59 6364 1534 0 0 1991 387 18 10 100 100 100 100 6935 7898 3.947 .253 .241 .269 .248 1.417 52 379 .238 .97 90 5000 17970 16 25 347 356 0 7491 298 7193 1.3 8168 7871 .769 1.237 .379 .307
20 904 176 78 58 826 118 920 177 83 60 842 119 0 0 323 37 25 11 100 100 100 100 944 961 7 .143 .141 .15 .142 1.433 52 322 .129 .93 80 5170 17970 17 25 365 373 0 903 298 605 .733 908 611 1.364 .725 -.448 -.464

Total number of rows: 16128

Table truncated, full table size 3504 Kbytes.




Supplementary data files not provided
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