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Sample GSM89992 Query DataSets for GSM89992
Status Public on Dec 30, 2005
Title Fraction 68-70
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 68-70
Organism Saccharomyces cerevisiae
Characteristics Fraction 68-70
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41745.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 1015 573 230 290 785 283 971 544 240 295 741 254 0 0 320 150 66 55 100 96 100 90 1068 995 2.774 .361 .343 .331 .344 1.466 32 236 .358 .91 70 1170 19100 42 49 21 28 0 1857 940 917 1.168 1763 823 .856 1.111 .224 .151
2 17554 391 207 270 17347 121 16866 377 225 278 16659 107 0 0 9319 108 74 58 100 71 100 47 17468 16766 143.364 .007 .006 .019 .014 1.996 80 469 .007 .71 100 1350 19100 41 51 38 48 0 1267 875 392 .023 1222 347 44.244 .021 -5.467 -5.586
3 19212 11915 130 201 19082 11714 20115 11829 125 164 19985 11628 0 0 8874 5883 79 113 100 100 100 100 30796 31613 1.629 .614 .582 .633 .659 1.825 80 446 .609 .95 100 1530 19100 41 51 56 66 0 38608 651 37957 1.989 38329 37678 .503 1.885 .992 .915
4 5682 668 47 36 5635 632 6207 704 49 37 6160 668 0 0 2055 201 19 7 100 100 100 100 6267 6828 8.916 .112 .108 .115 .111 1.219 32 224 .105 .97 70 1680 19090 41 48 72 79 0 2165 117 2048 .363 2281 2165 2.752 .351 -1.46 -1.509
5 2538 1411 48 36 2490 1375 2606 1480 49 37 2558 1444 0 0 390 241 17 19 100 100 100 100 3865 4002 1.811 .552 .565 .55 .548 1.155 52 384 .509 .96 90 1860 19090 40 49 89 98 0 4572 117 4455 1.789 4796 4679 .559 1.829 .839 .871
6 15750 1002 52 37 15698 965 16121 1035 54 37 16069 998 0 0 2391 140 11 6 100 100 100 100 16663 17067 16.267 .061 .062 .062 .062 1.1 52 380 .058 .97 90 2030 19090 40 49 106 115 0 3247 120 3127 .199 3354 3234 5.02 .201 -2.328 -2.313
7 2599 1177 56 40 2543 1137 2739 1222 57 42 2683 1182 0 0 533 166 11 15 100 100 100 100 3680 3865 2.237 .447 .441 .455 .441 1.178 52 398 .417 .97 90 2200 19080 39 48 123 132 0 3814 130 3684 1.449 3960 3830 .69 1.428 .535 .514
8 1921 962 57 38 1864 924 2017 956 58 38 1960 918 0 0 765 332 9 6 100 100 100 100 2788 2878 2.017 .496 .468 .525 .457 1.593 32 236 .471 .96 70 2370 19080 40 47 141 148 0 3117 123 2994 1.606 3098 2975 .623 1.518 .684 .602
9 555 655 64 44 491 611 691 755 70 82 627 711 0 0 282 355 28 114 93 83 87 76 1102 1338 .804 1.244 1.134 1.336 1.357 1.73 80 498 1.277 .94 100 2570 19080 39 49 160 170 -50 2122 143 1980 4.032 2446 2304 .248 3.674 2.012 1.878
10 743 487 98 110 645 377 771 478 107 115 673 368 0 0 131 59 31 19 100 100 100 100 1022 1041 1.711 .584 .547 .592 .633 1.188 12 104 .605 .92 50 2720 19080 41 46 177 182 0 1578 356 1222 1.894 1549 1192 .528 1.772 .921 .825
11 2403 267 81 94 2322 173 2529 287 81 85 2448 193 0 0 651 74 26 36 100 96 100 88 2495 2641 13.422 .075 .079 .073 .079 1.487 80 480 .08 .9 100 2900 19080 39 49 193 203 0 865 305 561 .241 930 625 4.142 .255 -2.05 -1.969
12 2425 3095 53 40 2372 3055 2772 3473 57 51 2719 3433 0 0 818 1239 17 28 100 100 100 100 5427 6152 .776 1.288 1.263 1.281 1.318 1.373 80 444 1.327 .97 100 3080 19070 38 48 211 221 0 10029 130 9899 4.173 11254 11124 .24 4.091 2.061 2.033
13 2751 380 49 37 2702 343 2899 393 50 37 2850 356 0 0 564 95 11 5 100 100 100 100 3045 3206 7.878 .127 .125 .124 .125 1.248 80 440 .125 .97 100 3250 19070 38 48 228 238 0 1231 120 1111 .411 1273 1154 2.431 .405 -1.282 -1.305
14 15474 9737 52 39 15422 9698 16838 9336 57 60 16786 9297 0 0 5374 4586 19 47 100 100 100 100 25120 26083 1.59 .629 .554 .584 .61 1.302 80 510 .655 .98 110 3420 19070 37 48 244 255 0 31551 126 31424 2.038 30251 30125 .491 1.795 1.027 .844
15 2650 1592 76 151 2574 1441 2800 1648 74 129 2724 1497 0 0 511 304 21 54 100 100 100 100 4015 4221 1.786 .56 .55 .56 .58 1.222 80 454 .554 .97 100 3600 19060 37 47 263 273 0 5159 489 4669 1.814 5340 4851 .551 1.781 .859 .832
16 2368 473 85 161 2283 312 2598 494 87 162 2513 333 0 0 688 124 15 17 100 98 100 96 2595 2846 7.317 .137 .133 .127 .139 1.478 80 452 .14 .97 100 3770 19070 38 48 280 290 0 1533 522 1011 .443 1601 1079 2.258 .429 -1.175 -1.22
17 724 315 91 164 633 151 718 321 94 165 627 157 0 0 115 33 19 19 100 100 100 100 784 784 4.192 .239 .25 .235 .243 1.229 52 390 .222 .94 90 3950 19050 36 45 298 307 0 1021 531 489 .773 1040 509 1.294 .811 -.372 -.302
18 4729 1543 85 158 4644 1385 4401 1528 89 161 4316 1370 0 0 2324 686 20 19 100 100 100 100 6029 5686 3.353 .298 .317 .295 .297 1.157 52 382 .295 .99 90 4120 19060 37 46 315 324 0 5000 512 4488 .966 4951 4439 1.035 1.029 -.049 .041
19 3670 16613 81 157 3589 16456 3876 17914 83 159 3795 17757 0 0 984 6463 17 22 100 100 100 100 20045 21552 .218 4.585 4.679 4.309 4.685 1.313 80 474 4.906 .98 100 4300 19060 37 47 333 343 0 53831 509 53322 14.857 58046 57538 .067 15.161 3.893 3.922
20 625 390 82 154 543 236 687 365 85 155 605 211 0 0 233 156 15 17 100 100 100 100 779 816 2.301 .435 .349 .441 .376 1.713 80 454 .418 .75 100 4480 19040 35 45 351 361 0 1264 499 765 1.408 1183 684 .71 1.13 .494 .176

Total number of rows: 16128

Table truncated, full table size 3487 Kbytes.




Supplementary data files not provided
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