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Sample GSM70936 Query DataSets for GSM70936
Status Public on Aug 20, 2005
Title Dauer MTC#2T7 (red, channel 2) vs. RefB-JW (green, channel 1)
Sample type RNA
 
Channel 1
Source name RefB-JW (green)
Organism Caenorhabditis elegans
Characteristics RefB-JW (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Dauer MTC#2T7 (red)
Organism Caenorhabditis elegans
Characteristics Dauer MTC#2T7 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11164.gif
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 Aug 18, 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 GPL2653
Series (1)
GSE3169 Global analysis of dauer gene expression in Caenorhabditis elegans

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
1 892 838 246 249 646 589 null null 4390 2505 null null null null null null null null 0 3 null null null null 1.097 .912 null null .839 null 32 236 .569 .97 null null null 48 55 30 37 -100 654 194 460 .712 null null 1.404 null -.49 null
2 5826 11463 231 249 5595 11214 null null 487 702 null null null null null null null null 100 100 null null null null .499 2.004 null null .492 null 32 227 1.831 .97 null null null 50 57 51 58 0 8955 194 8761 1.566 null null .639 null .647 null
3 837 784 203 245 634 539 null null 221 255 null null null null null null null null 100 100 null null null null 1.176 .85 null null 1.167 null 32 219 .769 .85 null null null 50 57 69 76 0 612 191 421 .664 null null 1.506 null -.591 null
4 8362 7728 205 237 8157 7491 null null 502 281 null null null null null null null null 80 100 null null null null 1.089 .918 null null 1.119 null 52 291 .909 .97 null null null 50 58 83 91 0 6037 185 5852 .717 null null 1.394 null -.479 null
5 13389 1707 213 259 13176 1448 null null 241 270 null null null null null null null null 100 94 null null null null 9.099 .11 null null 8.994 null 52 312 .103 .95 null null null 49 57 99 107 0 1333 202 1131 .086 null null 11.65 null -3.542 null
6 1878 563 217 252 1661 311 null null 223 260 null null null null null null null null 93 87 null null null null 5.341 .187 null null 2.603 null 32 170 .105 .84 null null null 49 55 116 122 0 439 196 243 .146 null null 6.835 null -2.773 null
7 9508 8326 208 240 9300 8086 null null 218 248 null null null null null null null null 100 100 null null null null 1.15 .869 null null 1.151 null 80 409 .816 .97 null null null 47 57 129 139 0 6504 187 6317 .679 null null 1.472 null -.558 null
8 218 262 231 268 -13 -6 null null 601 509 null null null null null null null null 0 0 null null null null null null null null 1.046 null 32 182 .759 .95 null null null 46 53 141 148 -100 204 209 -5 null null null null null null null
9 33987 1784 221 263 33766 1521 null null 321 324 null null null null null null null null 98 85 null null null null 22.2 .045 null null 22.578 null 80 457 .044 .97 null null null 46 56 162 172 0 1393 205 1188 .035 null null 28.423 null -4.829 null
10 5222 5580 215 267 5007 5313 null null 226 276 null null null null null null null null 100 100 null null null null .942 1.061 null null .944 null 52 275 .991 .97 null null null 47 55 178 186 0 4359 208 4151 .829 null null 1.206 null -.27 null
11 13688 8858 220 277 13468 8581 null null 372 294 null null null null null null null null 91 100 null null null null 1.57 .637 null null 1.576 null 80 445 .603 .97 null null null 46 56 193 203 0 6920 216 6704 .498 null null 2.009 null -1.006 null
12 4233 4107 225 279 4008 3828 null null 242 290 null null null null null null null null 100 100 null null null null 1.047 .955 null null 1.031 null 52 296 .853 .95 null null null 47 55 210 218 0 3208 217 2991 .746 null null 1.34 null -.422 null
13 11114 10258 223 274 10891 9984 null null 226 280 null null null null null null null null 100 100 null null null null 1.091 .917 null null 1.039 null 52 314 .857 .96 null null null 47 55 226 234 0 8014 214 7800 .716 null null 1.396 null -.482 null
14 1291 1072 221 286 1070 786 null null 229 293 null null null null null null null null 100 100 null null null null 1.361 .735 null null 1.181 null 32 232 .515 .8 null null null 46 53 242 249 0 837 223 614 .574 null null 1.743 null -.801 null
15 2533 2617 221 290 2312 2327 null null 254 318 null null null null null null null null 90 100 null null null null .994 1.006 null null .976 null 32 232 .771 .88 null null null 45 52 256 263 0 2044 226 1818 .786 null null 1.272 null -.347 null
16 2537 2101 220 310 2317 1791 null null 244 320 null null null null null null null null 98 100 null null null null 1.294 .773 null null 1.282 null 52 314 .727 .94 null null null 46 54 273 281 0 1641 242 1399 .604 null null 1.656 null -.728 null
17 12840 24580 221 318 12619 24262 null null 238 343 null null null null null null null null 96 100 null null null null .52 1.923 null null .558 null 52 365 1.786 .96 null null null 44 53 288 297 0 19203 248 18955 1.502 null null .666 null .587 null
18 2059 2889 226 337 1833 2552 null null 247 348 null null null null null null null null 98 100 null null null null .718 1.392 null null .694 null 52 304 1.253 .92 null null null 46 54 305 313 0 2257 263 1994 1.088 null null .919 null .121 null
19 7085 5866 243 341 6842 5525 null null 270 356 null null null null null null null null 100 100 null null null null 1.238 .808 null null 1.274 null 32 236 .691 .95 null null null 44 51 321 328 0 4582 266 4316 .631 null null 1.585 null -.665 null
20 17549 3778 246 346 17303 3432 null null 272 429 null null null null null null null null 100 100 null null null null 5.042 .198 null null 4.905 null 52 319 .192 .95 null null null 45 53 337 345 0 2951 270 2681 .155 null null 6.454 null -2.69 null

Total number of rows: 21504

Table truncated, full table size 5230 Kbytes.




Supplementary data files not provided
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