NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM65037 Query DataSets for GSM65037
Status Public on Jul 22, 2005
Title New N2 mixed stage (red, channel 2) vs.L2 N2 T1.1 (green, channel 1)
Sample type RNA
 
Channel 1
Source name L2 N2 T1.1 (green, channel 1)
Organism Caenorhabditis elegans
Characteristics L2 N2 T1.1 (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name New N2 mixed stage (red, channel 2)
Organism Caenorhabditis elegans
Characteristics New N2 mixed stage (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11075.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 Jul 21, 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)
GSE2974 Downstream targets of let-60 Ras 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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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 6240 9631 130 308 6110 9323 null null 137 311 null null null null null null null null 91 93 null null null null .655 1.526 null null 1.619 null 80 422 1.443 .98 null null null 32 43 53 64 0 10701 342 10359 1.695 null null .59 null .762 null
2 2438 2870 127 292 2311 2578 null null 216 618 null null null null null null null null 79 48 null null null null .896 1.116 null null 1.172 null 120 472 1.134 .96 null null null 30 43 69 82 0 3188 324 2864 1.239 null null .807 null .31 null
3 573 885 132 286 441 599 null null 137 295 null null null null null null null null 91 93 null null null null .736 1.358 null null 1.398 null 80 356 1.181 .89 null null null 30 41 86 97 0 983 317 666 1.51 null null .662 null .595 null
4 2404 3835 131 282 2273 3553 null null 134 285 null null null null null null null null 90 90 null null null null .64 1.563 null null 1.614 null 120 455 1.581 .98 null null null 28 41 101 114 0 4261 313 3948 1.737 null null .576 null .797 null
5 4705 3620 131 282 4574 3338 null null 136 285 null null null null null null null null 92 91 null null null null 1.37 .73 null null .751 null 120 387 .701 .95 null null null 31 43 117 129 0 4022 313 3709 .811 null null 1.233 null -.302 null
6 1392 1668 133 283 1259 1385 null null 139 289 null null null null null null null null 82 78 null null null null .909 1.1 null null 1.041 null 80 369 1.058 .96 null null null 30 40 134 144 0 1853 314 1539 1.222 null null .818 null .29 null
7 5281 5414 126 284 5155 5130 null null 134 287 null null null null null null null null 91 95 null null null null 1.005 .995 null null 1.027 null 120 468 .991 .98 null null null 29 42 149 162 0 6015 315 5700 1.106 null null .904 null .145 null
8 1600 1891 118 279 1482 1612 null null 126 284 null null null null null null null null 65 72 null null null null .919 1.088 null null 1.272 null 120 397 1.024 .95 null null null 30 42 165 177 0 2101 310 1791 1.209 null null .827 null .273 null
9 938 19786 117 271 821 19515 null null 123 276 null null null null null null null null 84 100 null null null null .042 23.77 null null 23.767 null 120 455 22.127 .95 null null null 29 42 181 194 0 21984 301 21683 26.41 null null .038 null 4.723 null
10 1225 4516 123 272 1102 4244 null null 130 277 null null null null null null null null 86 93 null null null null .26 3.851 null null 3.656 null 120 372 3.732 .95 null null null 30 42 197 209 0 5017 302 4715 4.279 null null .234 null 2.097 null
11 7174 7661 121 271 7053 7390 null null 127 277 null null null null null null null null 87 89 null null null null .954 1.048 null null 1.057 null 156 541 1.059 .98 null null null 29 43 213 227 0 8512 301 8211 1.164 null null .859 null .219 null
12 1346 1973 115 267 1231 1706 null null 119 272 null null null null null null null null 98 98 null null null null .722 1.386 null null 1.501 null 80 380 1.286 .95 null null null 30 41 230 241 0 2192 296 1896 1.54 null null .649 null .623 null
13 6250 6517 113 274 6137 6243 null null 118 276 null null null null null null null null 87 79 null null null null .983 1.017 null null 1.041 null 120 473 1.026 .97 null null null 30 42 247 259 0 7241 304 6937 1.13 null null .885 null .177 null
14 791 1211 117 284 674 927 null null 120 285 null null null null null null null null 93 93 null null null null .727 1.375 null null 1.448 null 80 364 1.262 .93 null null null 31 42 262 273 0 1345 315 1030 1.528 null null .654 null .612 null
15 3249 4595 119 290 3130 4305 null null 125 291 null null null null null null null null 90 82 null null null null .727 1.375 null null 1.805 null 120 446 .855 .8 null null null 31 43 279 291 0 5105 322 4783 1.528 null null .654 null .612 null
16 153 342 122 273 31 69 null null 126 276 null null null null null null null null 27 43 null null null null .449 2.226 null null 2.643 null 80 340 .913 .66 null null null 31 41 293 303 0 380 303 77 2.484 null null .403 null 1.313 null
17 8209 11312 118 248 8091 11064 null null 121 251 null null null null null null null null 95 89 null null null null .731 1.367 null null 1.318 null 120 436 1.378 .97 null null null 31 43 311 323 0 12568 275 12293 1.519 null null .658 null .603 null
18 991 1141 104 205 887 936 null null 108 211 null null null null null null null null 81 76 null null null null .948 1.055 null null 1.159 null 120 370 1.014 .96 null null null 31 43 326 338 0 1267 227 1040 1.172 null null .853 null .23 null
19 2013 3382 101 188 1912 3194 null null 105 190 null null null null null null null null 94 95 null null null null .599 1.671 null null 1.78 null 120 421 1.623 .96 null null null 30 43 341 354 0 3757 208 3549 1.856 null null .539 null .892 null
20 694 6942 103 174 591 6768 null null 106 178 null null null null null null null null 78 91 null null null null .087 11.452 null null 10.922 null 156 517 10.642 .95 null null null 29 43 358 372 0 7713 193 7520 12.724 null null .079 null 3.67 null

Total number of rows: 21504

Table truncated, full table size 5187 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap