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Sample GSM91456 Query DataSets for GSM91456
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 13 (48E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 13 (48E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 13 (48E)
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/2000-05/6421.gif
Measurement: time(absolute) 13 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 GPL3097
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
1 223 522 96 74 127 448 null null 97 75 null null null null null null null null 63 86 null null null null .283 3.528 null null 4.471 null 52 359 2.421 .85 null null null 95 104 65 74 0 297 42 255 2.008 null null .498 null 1.006 null
2 153 278 96 67 57 211 null null 98 69 null null null null null null null null 40 71 null null null null .27 3.702 null null 3.467 null 52 245 1.896 .8 null null null 93 101 82 90 0 158 38 120 2.107 null null .475 null 1.075 null
3 143 260 93 68 50 192 null null 96 70 null null null null null null null null 56 56 null null null null .26 3.84 null null 2.419 null 52 262 2.691 .71 null null null 92 101 97 106 0 148 39 109 2.186 null null .458 null 1.128 null
4 197 281 96 69 101 212 null null 99 74 null null null null null null null null 64 61 null null null null .476 2.099 null null 1.792 null 120 488 1.461 .88 null null null 92 104 110 122 0 160 39 121 1.195 null null .837 null .257 null
5 195 419 97 67 98 352 null null 100 68 null null null null null null null null 45 85 null null null null .278 3.592 null null 3.576 null 120 527 2.003 .82 null null null 92 104 126 138 0 238 38 200 2.044 null null .489 null 1.032 null
6 290 442 97 72 193 370 null null 99 73 null null null null null null null null 61 69 null null null null .522 1.917 null null 1.728 null 52 226 1.608 .9 null null null 91 99 146 154 0 252 41 211 1.091 null null .916 null .126 null
7 354 880 92 81 262 799 null null 95 84 null null null null null null null null 78 88 null null null null .328 3.05 null null 2.739 null 80 433 2.892 .94 null null null 91 102 159 170 0 501 46 455 1.736 null null .576 null .796 null
8 250 614 97 88 153 526 null null 111 91 null null null null null null null null 37 81 null null null null .291 3.438 null null 2.901 null 32 216 2.556 .84 null null null 93 100 177 184 0 349 50 299 1.957 null null .511 null .969 null
9 200 350 98 93 102 257 null null 110 93 null null null null null null null null 17 59 null null null null .397 2.52 null null 1.954 null 52 244 1.829 .87 null null null 95 103 194 202 0 199 53 146 1.434 null null .697 null .52 null
10 329 442 98 91 231 351 null null 99 92 null null null null null null null null 88 92 null null null null .658 1.519 null null 1.27 null 80 316 1.564 .93 null null null 94 105 207 218 0 252 52 200 .865 null null 1.156 null -.209 null
11 393 658 92 79 301 579 null null 95 81 null null null null null null null null 80 88 null null null null .52 1.924 null null 1.914 null 80 291 1.807 .96 null null null 92 102 223 233 0 375 45 330 1.095 null null .913 null .131 null
12 647 2518 97 71 550 2447 null null 99 73 null null null null null null null null 90 94 null null null null .225 4.449 null null 4.192 null 156 482 4.118 .93 null null null 90 104 237 251 0 1433 40 1393 2.532 null null .395 null 1.341 null
13 242 504 100 70 142 434 null null 101 72 null null null null null null null null 57 76 null null null null .327 3.056 null null 1.545 null 156 529 2.829 .76 null null null 90 104 253 267 0 287 40 247 1.74 null null .575 null .799 null
14 205 372 96 76 109 296 null null 99 79 null null null null null null null null 57 67 null null null null .368 2.716 null null 2.566 null 80 349 2.359 .87 null null null 94 104 271 281 0 212 43 168 1.546 null null .647 null .628 null
15 228 441 93 86 135 355 null null 97 88 null null null null null null null null 63 75 null null null null .38 2.63 null null 2.333 null 80 408 2.235 .93 null null null 91 101 289 299 0 251 49 202 1.497 null null .668 null .582 null
16 268 475 97 94 171 381 null null 99 95 null null null null null null null null 53 88 null null null null .449 2.228 null null 2.439 null 52 294 1.659 .9 null null null 91 100 304 313 -100 270 54 217 1.268 null null .789 null .343 null
17 323 562 98 87 225 475 null null 100 88 null null null null null null null null 70 85 null null null null .474 2.111 null null 2.063 null 80 417 1.817 .92 null null null 90 101 318 329 0 320 50 270 1.202 null null .832 null .265 null
18 323 504 100 78 223 426 null null 103 81 null null null null null null null null 88 98 null null null null .523 1.91 null null 1.985 null 52 291 1.492 .9 null null null 92 101 336 345 0 287 44 242 1.087 null null .92 null .121 null
19 257 429 98 89 159 340 null null 102 92 null null null null null null null null 69 75 null null null null .468 2.138 null null 1.866 null 52 224 1.779 .82 null null null 93 101 353 361 0 244 51 194 1.217 null null .822 null .284 null
20 434 590 95 99 339 491 null null 99 102 null null null null null null null null 75 83 null null null null .69 1.448 null null 1.155 null 80 356 1.438 .91 null null null 88 99 367 378 0 336 56 279 .824 null null 1.213 null -.279 null

Total number of rows: 21504

Table truncated, full table size 5062 Kbytes.




Supplementary data files not provided
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