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Sample GSM91463 Query DataSets for GSM91463
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 10 (47E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 10 (47E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 10 (47E)
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/2000-05/5800.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 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
1 615 480 228 65 387 415 null null 233 67 null null null null null null null null 92 94 null null null null .933 1.072 null null 1.102 null 52 376 .88 .91 null null null 189 198 88 97 0 484 65 419 1.083 null null .924 null .115 null
2 358 120 216 60 142 60 null null 217 61 null null null null null null null null 71 80 null null null null 2.367 .423 null null .5 null 52 299 .29 .78 null null null 189 197 105 113 0 121 60 61 .43 null null 2.328 null -1.219 null
3 290 80 214 60 76 20 null null 217 62 null null null null null null null null 30 53 null null null null 3.8 .263 null null .418 null 52 264 .168 .65 null null null 188 196 120 128 0 80 60 20 .263 null null 3.8 null -1.926 null
4 430 175 219 61 211 114 null null 223 62 null null null null null null null null 65 80 null null null null 1.851 .54 null null .537 null 120 520 .395 .88 null null null 186 198 133 145 0 176 61 115 .545 null null 1.835 null -.876 null
5 375 211 242 67 133 144 null null 254 71 null null null null null null null null 36 72 null null null null .924 1.083 null null 1.205 null 120 532 .557 .81 null null null 186 198 149 161 0 213 67 146 1.098 null null .911 null .135 null
6 505 167 263 75 242 92 null null 278 79 null null null null null null null null 46 73 null null null null 2.63 .38 null null .441 null 52 280 .244 .72 null null null 189 197 167 175 0 168 75 93 .384 null null 2.602 null -1.38 null
7 1247 1347 262 78 985 1269 null null 261 81 null null null null null null null null 94 100 null null null null .776 1.288 null null 1.161 null 52 232 1.137 .91 null null null 190 199 182 191 0 1360 78 1282 1.302 null null .768 null .38 null
8 203 67 221 72 null null null null 234 79 null null null null null null null null 1 0 null null null null null null null null .327 null 80 408 .248 .56 null null null 182 193 192 203 0 67 72 null null null null null null null null
9 230 71 243 76 null null null null 249 81 null null null null null null null null 2 0 null null null null null null null null .293 null 80 427 .002 0 null null null 182 193 208 219 0 71 76 null null null null null null null null
10 427 160 246 74 181 86 null null 247 75 null null null null null null null null 26 33 null null null null 2.105 .475 null null .379 null 80 376 .314 .8 null null null 182 193 224 235 0 161 74 87 .481 null null 2.08 null -1.057 null
11 246 72 248 71 null 1 null null 248 73 null null null null null null null null 10 12 null null null null null null null null .233 null 80 334 .009 .03 null null null 182 193 240 251 0 72 71 1 null null null null null null null
12 1119 2782 247 73 872 2709 null null 249 74 null null null null null null null null 52 72 null null null null .322 3.107 null null 2.99 null 120 374 2.485 .87 null null null 180 192 258 270 0 2810 73 2737 3.139 null null .319 null 1.65 null
13 242 70 241 73 1 null null null 244 74 null null null null null null null null 12 12 null null null null null null null null .438 null 80 326 .032 .09 null null null 181 192 272 283 0 70 73 null null null null null null null null
14 215 67 221 69 null null null null 208 69 null null null null null null null null 3 6 null null null null null null null null .264 null 80 409 .09 .34 null null null 181 192 288 299 0 67 69 null null null null null null null null
15 98 53 155 55 null null null null 135 57 null null null null null null null null 2 7 null null null null null null null null .096 null 80 414 .08 .44 null null null 181 192 304 315 0 53 55 null null null null null null null null
16 55 49 63 50 null null null null 89 51 null null null null null null null null 0 7 null null null null null null null null .714 null 80 461 .059 .17 null null null 180 191 320 331 -100 49 50 null null null null null null null null
17 429 379 56 50 373 329 null null 56 51 null null null null null null null null 59 63 null null null null 1.134 .882 null null .912 null 52 274 .69 .85 null null null 181 189 339 347 0 382 50 332 .89 null null 1.123 null -.168 null
18 65 53 56 49 9 4 null null 56 49 null null null null null null null null 17 20 null null null null 2.25 .444 null null .889 null 80 449 .077 .2 null null null 180 191 352 363 0 53 49 4 .444 null null 2.25 null -1.17 null
19 181 107 62 53 119 54 null null 104 62 null null null null null null null null 42 42 null null null null 2.204 .454 null null .299 null 156 613 .357 .66 null null null 182 196 372 386 0 108 53 55 .462 null null 2.164 null -1.113 null
20 1823 879 85 61 1738 818 null null 138 68 null null null null null null null null 92 92 null null null null 2.125 .471 null null .37 null 80 265 .39 .83 null null null 179 190 386 397 0 887 61 826 .475 null null 2.104 null -1.073 null

Total number of rows: 21504

Table truncated, full table size 5138 Kbytes.




Supplementary data files not provided
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