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Sample GSM89982 Query DataSets for GSM89982
Status Public on Dec 30, 2005
Title Fraction 98-100
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 98-100
Organism Saccharomyces cerevisiae
Characteristics Fraction 98-100
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41742.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 2232 588 157 90 2075 498 2257 601 157 90 2100 511 0 0 451 118 23 14 100 100 100 100 2573 2611 4.167 .24 .243 .239 .239 1.158 32 230 .236 .97 70 1580 17360 28 35 34 41 0 3120 478 2643 1.274 3189 2712 .785 1.291 .349 .369
2 23713 4532 153 91 23560 4441 23550 3888 155 92 23397 3797 0 0 7882 2636 23 16 100 100 100 100 28001 27194 5.305 .188 .162 .162 .168 1.569 52 328 .202 .94 80 1760 17370 29 37 52 60 0 24049 483 23566 1 20632 20149 1 .861 0 -.216
3 45203 6253 148 88 45055 6165 48374 6704 149 89 48226 6616 0 0 12047 1664 22 15 100 100 100 100 51220 54842 7.308 .137 .137 .139 .139 1.529 52 372 .131 .96 90 1940 17360 27 36 69 78 0 33182 467 32715 .726 35575 35108 1.377 .728 -.462 -.458
4 5850 1275 140 88 5710 1187 6645 1334 141 89 6505 1246 0 0 1975 451 21 16 100 100 100 100 6897 7751 4.81 .208 .192 .21 .216 1.657 52 305 .201 .95 80 2100 17360 28 36 86 94 0 6766 467 6299 1.103 7079 6612 .907 1.016 .142 .024
5 2179 424 146 88 2033 336 2277 451 147 87 2131 363 0 0 420 96 23 14 100 100 100 100 2369 2494 6.051 .165 .17 .16 .171 1.399 52 319 .161 .95 80 2260 17350 27 35 102 110 0 2250 467 1783 .877 2393 1926 1.14 .904 -.189 -.146
6 15690 2274 140 85 15550 2189 15986 2273 143 85 15846 2188 0 0 3037 219 23 14 100 100 100 100 17739 18034 7.104 .141 .138 .145 .138 1.297 52 318 .13 .96 80 2450 17350 27 35 121 129 0 12067 451 11616 .747 12062 11611 1.339 .733 -.421 -.449
7 2818 492 141 86 2677 406 2845 520 142 86 2704 434 0 0 401 117 25 14 100 100 100 100 3083 3138 6.594 .152 .161 .143 .151 1.377 52 318 .154 .95 80 2610 17350 27 35 137 145 0 2611 456 2154 .805 2759 2303 1.243 .852 -.313 -.232
8 2969 718 145 86 2824 632 3496 824 146 86 3351 738 0 0 1564 341 28 15 100 100 100 100 3456 4089 4.468 .224 .22 .245 .225 1.889 52 387 .216 .97 90 2790 17350 26 35 154 163 0 3810 456 3354 1.188 4373 3916 .842 1.169 .248 .225
9 883 422 146 87 737 335 899 430 150 90 753 343 0 0 100 55 34 19 100 100 100 100 1072 1096 2.2 .455 .456 .452 .462 1.236 52 401 .446 .94 90 2960 17360 27 36 171 180 0 2239 462 1778 2.412 2282 1820 .415 2.417 1.27 1.273
10 2531 749 155 91 2376 658 2462 745 161 92 2307 654 0 0 860 185 30 16 100 100 100 100 3034 2961 3.611 .277 .283 .284 .262 1.313 32 230 .257 .96 70 3140 17350 27 34 190 197 0 3975 483 3492 1.47 3953 3470 .68 1.504 .555 .589
11 2911 754 136 84 2775 670 3083 854 145 89 2947 770 0 0 779 239 32 44 100 98 100 94 3445 3717 4.142 .241 .261 .225 .256 1.593 52 328 .239 .95 80 3300 17350 27 35 206 214 0 4001 446 3555 1.281 4532 4086 .781 1.387 .358 .471
12 3771 831 127 82 3644 749 3891 899 132 83 3764 817 0 0 666 236 26 16 100 100 100 100 4393 4581 4.865 .206 .217 .192 .215 1.454 52 320 .207 .95 80 3480 17340 26 34 224 232 0 4410 435 3975 1.091 4771 4335 .917 1.152 .125 .204
13 2762 512 132 85 2630 427 2739 523 134 85 2607 438 0 0 393 70 22 15 100 100 100 100 3057 3045 6.159 .162 .168 .161 .171 1.249 52 396 .159 .96 90 3660 17350 26 35 241 250 0 2717 451 2266 .862 2775 2324 1.161 .892 -.215 -.166
14 31092 2369 133 85 30959 2284 33052 2458 135 85 32919 2373 0 0 5920 409 24 14 100 100 100 100 33243 35292 13.555 .074 .072 .074 .074 1.081 52 366 .069 .98 90 3830 17330 24 33 258 267 0 12571 451 12120 .391 13043 12592 2.554 .383 -1.353 -1.386
15 3102 547 131 83 2971 464 3042 558 132 83 2911 475 0 0 564 72 21 13 100 100 100 100 3435 3386 6.403 .156 .163 .157 .154 1.238 52 364 .143 .95 90 3990 17330 24 33 274 283 0 2903 440 2462 .829 2961 2521 1.207 .866 -.271 -.208
16 2016 391 131 82 1885 309 2362 444 133 82 2231 362 0 0 867 136 22 14 100 98 100 95 2194 2593 6.1 .164 .162 .166 .164 1.892 80 480 .157 .97 100 4170 17330 24 34 292 302 0 2075 435 1640 .87 2356 1921 1.15 .861 -.201 -.216
17 1261 718 133 81 1128 637 1228 732 134 82 1095 651 0 0 205 81 23 14 100 100 100 100 1765 1746 1.771 .565 .595 .569 .565 1.134 52 372 .537 .97 90 4350 17330 24 33 310 319 0 3810 430 3380 2.997 3884 3455 .334 3.155 1.583 1.658
18 4907 685 124 80 4783 605 5053 736 125 81 4929 656 0 0 1716 204 20 15 100 100 100 100 5388 5585 7.906 .126 .133 .125 .123 1.282 52 314 .121 .98 80 4520 17330 25 33 328 336 0 3635 425 3210 .671 3906 3481 1.49 .706 -.575 -.502
19 6483 674 131 81 6352 593 6330 680 139 83 6199 599 0 0 827 94 48 17 100 100 100 100 6945 6798 10.712 .093 .097 .093 .094 1.185 52 381 .091 .97 90 4700 17330 24 33 345 354 0 3577 430 3147 .495 3608 3179 2.019 .513 -1.013 -.964
20 1416 673 132 82 1284 591 1434 665 137 83 1302 583 0 0 289 100 32 17 100 100 100 100 1875 1885 2.173 .46 .448 .466 .463 1.181 52 358 .442 .97 90 4870 17320 23 32 362 371 0 3571 435 3136 2.442 3529 3094 .409 2.376 1.288 1.249

Total number of rows: 16128

Table truncated, full table size 3581 Kbytes.




Supplementary data files not provided
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