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Sample GSM89997 Query DataSets for GSM89997
Status Public on Dec 30, 2005
Title Fraction 94-96 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 94-96
Organism Saccharomyces cerevisiae
Characteristics Fraction 94-96
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41755.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
1 329 137 57 54 272 83 263 127 59 55 206 73 0 0 164 58 8 13 100 94 100 86 355 279 3.277 .305 .354 .276 .321 2.064 52 301 .295 .87 80 1670 18540 18 26 55 63 0 464 183 281 1.033 430 247 .968 1.2 .047 .263
2 9017 4044 61 56 8956 3988 7752 3029 64 58 7691 2973 0 0 5434 2913 27 16 100 100 100 100 12944 10664 2.246 .445 .387 .395 .387 1.994 52 392 .448 .93 90 1830 18530 16 25 70 79 0 13691 190 13501 1.507 10255 10065 .663 1.309 .592 .388
3 14404 2386 62 52 14342 2334 12716 1962 65 54 12654 1910 0 0 7233 1530 27 15 100 100 100 100 16676 14564 6.145 .163 .151 .144 .153 1.584 52 401 .166 .94 90 2020 18530 16 25 89 98 0 8078 176 7902 .551 6642 6466 1.815 .511 -.86 -.969
4 5231 2996 60 54 5171 2942 5488 3119 60 55 5428 3065 0 0 1490 766 10 12 100 100 100 100 8113 8493 1.758 .569 .565 .577 .537 1.34 52 380 .541 .95 90 2190 18540 17 26 106 115 0 10143 183 9960 1.926 10559 10376 .519 1.912 .946 .935
5 2362 542 60 54 2302 488 2666 587 62 55 2606 533 0 0 1012 201 10 13 100 100 100 100 2790 3139 4.717 .212 .205 .218 .205 1.55 52 322 .195 .94 80 2360 18540 18 26 124 132 0 1835 183 1652 .718 1987 1804 1.393 .692 -.479 -.53
6 12617 3293 61 55 12556 3238 14038 3643 63 57 13977 3588 0 0 3499 932 12 14 100 100 100 100 15794 17565 3.878 .258 .257 .257 .26 1.303 52 395 .248 .96 90 2540 18540 17 26 141 150 0 11148 186 10962 .873 12333 12147 1.145 .869 -.196 -.202
7 2588 642 62 55 2526 587 2772 676 63 57 2710 621 0 0 673 140 10 13 100 100 100 100 3113 3331 4.303 .232 .229 .234 .223 1.335 52 334 .213 .94 80 2720 18540 18 26 160 168 0 2173 186 1987 .787 2289 2102 1.271 .776 -.346 -.366
8 973 488 62 56 911 432 758 419 63 57 696 363 0 0 627 333 10 13 100 96 100 96 1343 1059 2.109 .474 .522 .377 .428 2.08 52 320 .477 .94 80 2900 18540 18 26 178 186 0 1652 190 1463 1.605 1419 1229 .623 1.766 .683 .82
9 811 611 60 56 751 555 904 650 60 56 844 594 0 0 261 192 9 13 100 100 100 100 1306 1438 1.353 .739 .704 .755 .715 1.903 52 320 .724 .93 80 3060 18540 18 26 194 202 0 2069 190 1879 2.502 2201 2011 .4 2.383 1.323 1.253
10 329 184 57 55 272 129 296 177 58 56 239 122 0 0 156 68 9 12 100 96 100 96 401 361 2.109 .474 .51 .494 .479 1.656 32 236 .424 .89 70 3240 18550 19 26 212 219 0 623 186 437 1.606 599 413 .623 1.728 .683 .789
11 3648 2486 56 55 3592 2431 3878 2578 57 55 3822 2523 0 0 1222 651 9 13 100 100 100 100 6023 6345 1.478 .677 .66 .698 .679 1.506 52 400 .659 .93 90 3420 18540 17 26 229 238 0 8416 186 8230 2.291 8728 8541 .436 2.235 1.196 1.16
12 4048 1404 57 55 3991 1349 4122 1429 57 55 4065 1374 0 0 998 310 7 12 100 100 100 100 5340 5439 2.958 .338 .338 .341 .347 1.35 52 386 .322 .94 90 3600 18540 17 26 247 256 0 4753 186 4567 1.144 4838 4652 .874 1.144 .194 .194
13 3521 1010 59 58 3462 952 3682 1031 60 58 3623 973 0 0 1072 259 10 13 100 100 100 100 4414 4596 3.637 .275 .269 .279 .262 1.328 52 379 .262 .96 90 3770 18540 17 26 264 273 0 3419 196 3223 .931 3490 3294 1.074 .909 -.103 -.137
14 12394 1781 59 57 12335 1724 14972 1785 60 58 14913 1728 0 0 7635 1176 11 14 100 97 100 95 14059 16641 7.155 .14 .116 .12 .139 2.426 80 474 .134 .92 100 3950 18540 17 27 282 292 0 6029 193 5837 .473 6043 5850 2.113 .392 -1.08 -1.35
15 3949 771 59 54 3890 717 3938 772 60 57 3879 718 0 0 954 177 9 19 100 100 100 100 4607 4597 5.425 .184 .185 .184 .184 1.354 52 371 .174 .93 90 4120 18540 17 26 299 308 0 2610 183 2427 .624 2614 2431 1.603 .627 -.68 -.674
16 2624 654 61 59 2563 595 2906 706 62 60 2845 647 0 0 767 194 10 14 100 100 100 98 3158 3492 4.308 .232 .227 .223 .229 1.564 52 387 .222 .96 90 4290 18540 17 26 316 325 0 2214 200 2014 .786 2390 2190 1.272 .77 -.348 -.377
17 1481 1034 61 57 1420 977 1474 1094 62 59 1413 1037 0 0 467 369 9 14 100 100 100 100 2397 2450 1.453 .688 .734 .666 .681 1.519 52 401 .69 .93 90 4470 18540 17 26 334 343 0 3501 193 3308 2.329 3704 3511 .429 2.485 1.22 1.313
18 2860 865 63 61 2797 804 1601 623 64 62 1538 562 0 0 2348 616 10 14 100 100 100 100 3601 2100 3.479 .287 .365 .305 .274 1.611 52 322 .266 .96 80 4640 18550 19 27 352 360 0 2928 207 2722 .973 2109 1903 1.028 1.237 -.039 .307
19 6359 1091 60 58 6299 1033 6872 1215 62 60 6812 1157 0 0 2675 379 10 14 100 100 100 100 7332 7969 6.098 .164 .17 .172 .159 1.496 52 380 .151 .95 90 4810 18550 18 27 368 377 0 3694 196 3497 .555 4113 3917 1.801 .575 -.849 -.798
20 1151 2151 61 59 1090 2092 1191 2168 65 61 1130 2109 0 0 419 698 21 16 100 100 100 100 3182 3239 .521 1.919 1.866 2 1.93 1.426 52 380 1.918 .95 90 4980 18550 18 27 385 394 0 7282 200 7082 6.498 7340 7140 .154 6.319 2.7 2.66

Total number of rows: 16128

Table truncated, full table size 3474 Kbytes.




Supplementary data files not provided
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