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Sample GSM91453 Query DataSets for GSM91453
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 9 (3E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 9 (3E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 9 (3E)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 ref. JL1
Organism Caenorhabditis elegans
Characteristics N2 ref. JL1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: aging, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3445.gif
Measurement: time(absolute) 10 d
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3098
Series (1)
GSE4005 Aging time course

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 1252 2218 118 71 1134 2147 null null 127 97 null null null null null null null null 68 62 null null null null .528 1.893 null null 1.824 null 80 412 1.505 .808 null null null 47 57 116 126 0 2583 83 2501 2.205 null null .453 null 1.141 null
2 757 1072 128 80 629 992 null null 134 105 null null null null null null null null 71 71 null null null null .634 1.577 null null 1.915 null 52 280 1.046 .704 null null null 48 57 132 141 0 1249 93 1155 1.837 null null .544 null .877 null
3 584 763 129 77 455 686 null null 135 94 null null null null null null null null 67 56 null null null null .663 1.508 null null 1.013 null 52 292 1.281 .527 null null null 47 55 148 156 0 889 90 799 1.756 null null .569 null .812 null
4 2375 1439 126 77 2249 1362 null null 131 88 null null null null null null null null 86 75 null null null null 1.651 .606 null null .746 null 80 410 .352 .612 null null null 47 57 165 175 0 1676 90 1586 .705 null null 1.418 null -.503 null
5 985 2027 128 80 857 1947 null null 135 90 null null null null null null null null 76 91 null null null null .44 2.272 null null 2.318 null 80 404 1.872 .872 null null null 46 57 180 191 0 2361 93 2268 2.646 null null .378 null 1.404 null
6 921 1245 127 89 794 1156 null null 133 105 null null null null null null null null 65 65 null null null null .687 1.456 null null 1.586 null 80 337 1.004 .702 null null null 47 57 197 207 0 1450 104 1346 1.696 null null .59 null .762 null
7 1407 1992 128 88 1279 1904 null null 135 110 null null null null null null null null 91 86 null null null null .672 1.489 null null 1.368 null 156 695 1.259 .835 null null null 44 59 210 225 0 2320 103 2218 1.734 null null .577 null .794 null
8 881 725 134 90 747 635 null null 142 102 null null null null null null null null 77 57 null null null null 1.176 .85 null null 1.012 null 80 367 .769 .778 null null null 46 57 226 237 0 844 105 740 .99 null null 1.01 null -.014 null
9 732 1030 136 83 596 947 null null 141 99 null null null null null null null null 76 73 null null null null .629 1.589 null null 1.5 null 52 298 1.291 .81 null null null 47 56 244 253 0 1200 97 1103 1.851 null null .54 null .888 null
10 1122 915 139 77 983 838 null null 146 98 null null null null null null null null 81 61 null null null null 1.173 .852 null null .737 null 120 398 .773 .816 null null null 46 58 261 273 0 1066 90 976 .993 null null 1.007 null -.01 null
11 1002 797 136 77 866 720 null null 142 95 null null null null null null null null 91 81 null null null null 1.203 .831 null null .818 null 156 563 .778 .823 null null null 45 60 274 289 0 928 90 839 .968 null null 1.033 null -.046 null
12 1648 7097 141 72 1507 7025 null null 151 89 null null null null null null null null 62 85 null null null null .215 4.662 null null 3.965 null 120 469 3.729 .822 null null null 46 59 291 304 0 8266 84 8183 5.43 null null .184 null 2.441 null
13 1452 1373 142 65 1310 1308 null null 155 84 null null null null null null null null 68 83 null null null null 1.002 .998 null null .911 null 80 385 .7 .74 null null null 47 58 308 319 0 1599 76 1524 1.163 null null .86 null .218 null
14 1130 1062 148 65 982 997 null null 154 82 null null null null null null null null 68 68 null null null null .985 1.015 null null 1.087 null 80 370 .775 .727 null null null 48 58 324 334 0 1237 76 1161 1.183 null null .846 null .242 null
15 1041 1011 145 65 896 946 null null 151 82 null null null null null null null null 76 75 null null null null .947 1.056 null null 1.047 null 80 430 .709 .728 null null null 47 58 340 351 0 1178 76 1102 1.23 null null .813 null .298 null
16 1517 1142 156 66 1361 1076 null null 160 85 null null null null null null null null 71 77 null null null null 1.265 .791 null null .888 null 80 427 .62 .799 null null null 47 58 356 367 -100 1330 77 1253 .921 null null 1.086 null -.119 null
17 3235 2130 151 70 3084 2060 null null 157 90 null null null null null null null null 91 88 null null null null 1.497 .668 null null .757 null 80 418 .52 .788 null null null 47 58 372 383 0 2481 82 2399 .778 null null 1.285 null -.362 null
18 1236 986 140 71 1096 915 null null 148 87 null null null null null null null null 90 83 null null null null 1.198 .835 null null .856 null 80 428 .635 .754 null null null 47 58 388 399 0 1148 83 1066 .972 null null 1.028 null -.04 null
19 1251 819 143 66 1108 753 null null 147 78 null null null null null null null null 70 67 null null null null 1.471 .68 null null .836 null 80 403 .504 .763 null null null 47 58 404 415 0 954 77 877 .792 null null 1.263 null -.337 null
20 6271 2169 150 68 6121 2101 null null 156 85 null null null null null null null null 80 66 null null null null 2.913 .343 null null .516 null 120 415 .25 .723 null null null 47 59 420 432 0 2526 79 2447 .4 null null 2.501 null -1.323 null

Total number of rows: 21120

Table truncated, full table size 5041 Kbytes.




Supplementary data files not provided
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