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Sample GSM91447 Query DataSets for GSM91447
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 3 (1E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 3 (1E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 3 (1E)
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/2000-03/3139.gif
Measurement: time(absolute) 3 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 2355 2048 208 115 2147 1933 null null 232 149 null null null null null null null null 63 67 null null null null 1.111 .9 null null 1.135 null 80 431 .612 .69 null null null 75 85 113 123 0 1657 93 1564 .729 null null 1.373 null -.457 null
2 647 997 191 104 456 893 null null 231 170 null null null null null null null null 61 53 null null null null .511 1.958 null null 1.991 null 52 300 .754 .442 null null null 76 85 129 138 0 807 84 723 1.585 null null .631 null .664 null
3 601 689 213 110 388 579 null null 250 137 null null null null null null null null 50 55 null null null null .67 1.492 null null 1.069 null 52 281 .795 .639 null null null 77 85 145 153 0 558 89 469 1.208 null null .828 null .272 null
4 1603 1724 229 114 1374 1610 null null 264 140 null null null null null null null null 53 60 null null null null .853 1.172 null null 1.09 null 80 426 .803 .702 null null null 76 86 162 172 0 1395 92 1303 .948 null null 1.055 null -.077 null
5 3170 2361 232 121 2938 2240 null null 266 147 null null null null null null null null 73 77 null null null null 1.312 .762 null null .836 null 80 414 .539 .704 null null null 75 86 178 189 0 1910 98 1813 .617 null null 1.621 null -.697 null
6 1097 1087 210 120 887 967 null null 230 151 null null null null null null null null 61 69 null null null null .917 1.09 null null .88 null 52 270 .859 .771 null null null 75 84 193 202 0 880 97 782 .882 null null 1.134 null -.181 null
7 1263 2885 209 132 1054 2753 null null 241 156 null null null null null null null null 62 70 null null null null .383 2.612 null null 2.579 null 208 905 2.119 .826 null null null 74 90 207 223 0 2334 107 2228 2.114 null null .473 null 1.08 null
8 761 654 202 126 559 528 null null 245 206 null null null null null null null null 56 28 null null null null 1.059 .945 null null .972 null 80 302 .598 .615 null null null 77 87 226 236 0 529 102 427 .764 null null 1.308 null -.388 null
9 634 784 199 125 435 659 null null 230 220 null null null null null null null null 56 30 null null null null .66 1.515 null null 1.29 null 52 308 1.014 .706 null null null 76 85 241 250 0 634 101 533 1.226 null null .816 null .294 null
10 1240 1933 195 148 1045 1785 null null 209 181 null null null null null null null null 80 67 null null null null .585 1.708 null null 1.72 null 80 404 1.47 .718 null null null 75 86 258 269 0 1564 120 1444 1.382 null null .723 null .467 null
11 709 979 214 145 495 834 null null 233 165 null null null null null null null null 80 80 null null null null .594 1.685 null null 1.337 null 156 546 1.447 .731 null null null 76 90 272 286 0 792 117 675 1.363 null null .733 null .447 null
12 1792 12845 229 139 1563 12706 null null 249 161 null null null null null null null null 67 92 null null null null .123 8.129 null null 8.474 null 120 453 6.251 .781 null null null 77 89 290 302 0 10394 112 10281 6.578 null null .152 null 2.718 null
13 1306 701 236 138 1070 563 null null 252 160 null null null null null null null null 81 76 null null null null 1.901 .526 null null .584 null 80 396 .414 .718 null null null 78 88 307 317 0 567 112 456 .426 null null 2.349 null -1.232 null
14 820 531 233 134 587 397 null null 262 154 null null null null null null null null 60 67 null null null null 1.479 .676 null null .688 null 80 365 .421 .639 null null null 78 88 323 333 0 430 108 321 .547 null null 1.827 null -.87 null
15 691 561 243 159 448 402 null null 269 177 null null null null null null null null 72 67 null null null null 1.114 .897 null null .881 null 80 371 .467 .319 null null null 79 89 339 349 0 454 129 325 .726 null null 1.377 null -.462 null
16 955 1166 275 199 680 967 null null 312 221 null null null null null null null null 70 72 null null null null .703 1.422 null null 1.54 null 80 431 1.081 .691 null null null 77 88 354 365 -100 944 161 782 1.151 null null .869 null .203 null
17 2504 1890 274 183 2230 1707 null null 308 204 null null null null null null null null 80 81 null null null null 1.306 .765 null null .858 null 80 400 .572 .745 null null null 78 89 370 381 0 1529 148 1381 .619 null null 1.614 null -.691 null
18 950 1070 231 157 719 913 null null 253 171 null null null null null null null null 62 68 null null null null .788 1.27 null null 1.251 null 80 426 .848 .696 null null null 78 89 385 396 0 866 127 739 1.028 null null .973 null .039 null
19 764 756 222 150 542 606 null null 240 171 null null null null null null null null 52 56 null null null null .894 1.118 null null .944 null 80 409 .654 .606 null null null 78 89 402 413 0 612 121 490 .905 null null 1.105 null -.144 null
20 3568 2144 216 136 3352 2008 null null 235 160 null null null null null null null null 53 60 null null null null 1.669 .599 null null .691 null 120 402 .394 .686 null null null 78 90 418 430 0 1735 110 1625 .485 null null 2.063 null -1.045 null

Total number of rows: 21120

Table truncated, full table size 5067 Kbytes.




Supplementary data files not provided
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