NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM89988 Query DataSets for GSM89988
Status Public on Dec 30, 2005
Title Fraction 86-88
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 86-88
Organism Saccharomyces cerevisiae
Characteristics Fraction 86-88
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41736.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 1609 408 127 68 1482 340 1649 422 127 68 1522 354 0 0 453 110 27 9 100 100 100 100 1822 1876 4.359 .229 .233 .227 .225 1.23 32 230 .224 .97 70 1460 17290 25 32 30 37 0 2678 446 2232 1.506 2770 2324 .664 1.527 .591 .61
2 18088 5727 132 68 17956 5659 16009 4033 133 68 15877 3965 0 0 6544 3089 22 9 100 100 100 100 23615 19842 3.173 .315 .25 .293 .288 1.326 52 334 .331 .96 80 1630 17300 26 34 47 55 0 37590 446 37144 2.069 26471 26025 .483 1.639 1.049 .713
3 36977 3619 139 68 36838 3551 37071 3402 141 68 36932 3334 0 0 12580 1746 28 8 100 100 100 100 40389 40266 10.374 .096 .09 .088 .092 1.372 52 334 .099 .97 80 1820 17300 26 34 66 74 0 23754 446 23308 .633 22330 21883 1.581 .593 -.66 -.755
4 10077 2468 139 67 9938 2401 9987 2650 142 68 9848 2583 0 0 3161 785 25 8 100 100 100 100 12339 12431 4.139 .242 .262 .24 .241 1.256 52 312 .237 .98 80 1990 17290 25 33 83 91 0 16199 440 15759 1.586 17394 16954 .631 1.722 .665 .784
5 3983 456 137 67 3846 389 4094 465 140 67 3957 398 0 0 1092 78 28 9 100 100 100 100 4235 4355 9.887 .101 .101 .104 .105 1.284 52 378 .095 .97 90 2150 17290 24 33 98 107 0 2993 440 2553 .664 3052 2612 1.506 .66 -.591 -.599
6 23192 5339 150 70 23042 5269 23757 5530 152 79 23607 5460 0 0 3683 628 35 72 100 100 100 100 28311 29067 4.373 .229 .231 .23 .23 1.143 52 326 .221 .99 80 2330 17290 25 33 117 125 0 35043 459 34584 1.501 36297 35838 .666 1.518 .586 .602
7 4527 558 146 71 4381 487 4602 532 150 83 4456 461 0 0 1127 210 32 53 100 100 100 100 4868 4917 8.996 .111 .103 .109 .106 1.265 52 326 .125 .81 80 2500 17290 25 33 134 142 0 3663 466 3197 .73 3492 3026 1.371 .679 -.455 -.558
8 1977 629 152 72 1825 557 2022 686 160 112 1870 614 0 0 1114 401 49 125 100 76 98 71 2382 2484 3.276 .305 .328 .26 .262 2.145 52 326 .275 .77 80 2680 17290 25 33 152 160 0 4129 473 3656 2.003 4503 4030 .499 2.155 1.002 1.108
9 1220 664 144 67 1076 597 1244 654 155 79 1100 587 0 0 332 160 60 54 100 100 98 100 1673 1687 1.802 .555 .534 .57 .547 1.281 52 381 .544 .95 90 2850 17300 25 34 168 177 0 4358 440 3919 3.642 4293 3853 .275 3.503 1.865 1.808
10 1525 420 132 65 1393 355 1599 409 141 77 1467 344 0 0 371 153 56 47 100 100 100 100 1748 1811 3.924 .255 .234 .243 .234 1.372 32 170 .244 .89 60 3020 17290 26 32 187 193 0 2757 427 2330 1.673 2685 2258 .598 1.539 .742 .622
11 5437 1779 128 59 5309 1720 5692 1824 133 64 5564 1765 0 0 1167 283 34 24 100 100 100 100 7029 7329 3.087 .324 .317 .328 .321 1.217 52 332 .313 .98 80 3190 17290 25 33 203 211 0 11677 387 11290 2.126 11972 11585 .47 2.082 1.088 1.058
12 5928 1463 120 59 5808 1404 6463 1524 124 73 6343 1465 0 0 1868 436 31 158 100 100 100 98 7212 7808 4.137 .242 .231 .253 .243 1.336 52 381 .232 .97 90 3370 17280 23 32 220 229 0 9603 387 9215 1.587 10003 9616 .63 1.516 .666 .6
13 4797 1120 120 59 4677 1061 4990 1148 127 92 4870 1089 0 0 978 142 40 187 100 100 100 100 5738 5959 4.408 .227 .224 .23 .225 1.181 52 371 .214 .97 90 3540 17290 24 33 237 246 0 7351 387 6964 1.489 7535 7148 .672 1.468 .574 .554
14 33821 2912 121 58 33700 2854 34796 3153 130 94 34675 3095 0 0 8398 664 77 191 100 100 100 100 36554 37770 11.808 .085 .089 .085 .084 1.209 52 372 .082 .98 90 3700 17280 23 32 253 262 0 19113 381 18733 .556 20695 20315 1.799 .586 -.847 -.771
15 6109 612 86 51 6023 561 6301 650 98 103 6215 599 0 0 1483 121 74 279 100 96 100 67 6584 6814 10.736 .093 .096 .094 .093 1.216 52 389 .084 .62 90 3880 17290 24 33 271 280 0 4017 335 3682 .611 4266 3932 1.636 .633 -.71 -.661
16 3930 853 84 49 3846 804 3944 868 89 50 3860 819 0 0 741 78 26 8 100 100 100 100 4650 4679 4.784 .209 .212 .213 .207 1.192 52 381 .197 .98 90 4050 17280 23 32 288 297 0 5599 322 5277 1.372 5697 5376 .729 1.393 .456 .478
17 1929 1464 97 52 1832 1412 1941 1493 103 52 1844 1441 0 0 402 213 31 9 100 100 100 100 3244 3285 1.297 .771 .781 .784 .773 1.184 52 380 .745 .98 90 4230 17280 23 32 306 315 0 9609 341 9268 5.059 9800 9458 .198 5.129 2.339 2.359
18 6183 480 89 50 6094 430 5528 473 93 50 5439 423 0 0 3282 214 26 8 100 100 100 100 6524 5862 14.172 .071 .078 .073 .07 1.299 52 314 .068 .98 80 4400 17280 24 32 324 332 0 3151 328 2822 .463 3105 2776 2.159 .51 -1.11 -.97
19 11476 1260 108 52 11368 1208 11507 1261 110 52 11399 1209 0 0 2172 294 28 7 100 100 100 100 12576 12608 9.411 .106 .106 .105 .106 1.205 52 387 .105 .98 90 4580 17290 24 33 341 350 0 8270 341 7929 .697 8277 7935 1.434 .696 -.52 -.523
20 1962 253 115 52 1847 201 1965 254 117 53 1850 202 0 0 413 34 22 8 100 100 100 100 2048 2052 9.189 .109 .109 .11 .11 1.198 52 308 .103 .97 80 4750 17280 24 32 359 367 0 1661 341 1319 .714 1667 1326 1.4 .717 -.485 -.481

Total number of rows: 16128

Table truncated, full table size 3547 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap